Biology subjects

Chatterjee, S.

Publications and source records attributed to Chatterjee, S..

177 records · Page 10Linked to original sources

bioRxiv2019

MTOC clustering and nuclear division through proper spindle positioning in yeast: a microtubule grow-and-catch model

The dynamic process of mitotic spindle assembly depends on multitudes of inter-dependent interactions involving kinetochores (KTs), microtubules (MTs), spindle pole bodies (SPBs), and molecular motors. Before forming the mitotic spindle, multiple visible microtubule organizing centers (MTOCs) coalesce into a single focus to serve as a SPB in the pathogenic budding yeast, Cryptococcus neoformans. To explain this unusual phenomenon in the fungal kingdom, we propose a search and capture model, in which cytoplasmic MTs (cMTs) nucleated by MTOCs grow and capture each other to promote MTOC clustering. Our quantitative modeling identifies multiple redundant mechanisms mediated by a combination of cMT-cell cortex interactions and inter-cMT coupling to facilitate MTOC clustering within the physiological time limit as determined by time-lapse live-cell microscopy. Besides, we screen various possible mechanisms by computational modeling and propose optimal conditions that favor proper spindle positioning - a critical determinant for timely chromosome segregation. These analyses also reveal that a combined effect of MT buckling, dynein pull, and cortical push maintains spatiotemporal spindle localization.

biophysics↗

bioRxiv2019

Channeling macrophage polarization by using a selective translation inhibitor

Macrophages contribute to host immunity and tissue homeostasis via alternative activation programs. M1-like macrophages control intracellular bacterial pathogens and tumor progression. In contrast, M2-like macrophages shape reparative microenvironments that can be conducive for pathogen survival or tumor growth. An imbalance of these macrophages phenotypes may perpetuate sites of chronic unresolved inflammation, such as infectious granulomas and solid tumors. We have found that plant-derived and synthetic rocaglates sensitize macrophages to low concentrations of the M1-inducing cytokine IFN-gamma and inhibit their responsiveness to IL-4, a prototypical activator of the M2-like phenotype. Treatement of primary macrophages with rocaglates increased their resilience to oxidative stress, stimulated autophagy and killing of intracellular mycobacteria. Thus, rocaglates represent a novel class of immunomodulators that can direct macrophage polarization towards the M1-like phenotype in complex microenvironments associated with hypofunction of type 1 and/or hyperactivation of type 2 immunity, e.g. chronic bacterial infections, allergies and, possibly, certain tumors.

immunology↗

bioRxiv2019

Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST

Chemolithotrophic bacteria oxidize various sulfur species for energy and electrons, thereby operationalizing biogeochemical sulfur cycles in nature. The best-studied pathway of bacterial sulfur-chemolithotrophy, involving direct oxidation of thiosulfate to sulfate (without any free intermediate) by the SoxXAYZBCD multienzyme system, is apparently the exclusive mechanism of thiosulfate oxidation in facultatively chemolithotrophic alphaproteobacteria. Here we explore the molecular mechanisms of sulfur oxidation in the thiosulfate- and tetrathionate-oxidizing alphaproteobacterium Paracoccus thiocyanatus SST, and compare them with the prototypical Sox process characterized in Paracoccus pantotrophus. Our results revealed the unique case where, an alphaproteobacterium has Sox as its secondary pathway of thiosulfate oxidation, converting [~]10% of the thiosulfate supplied whilst 90% of the substrate is oxidized via a Tetrathionate-Intermediate pathway. Knock-out mutation, followed by the study of sulfur oxidation kinetics, showed that thiosulfate-to-tetrathionate conversion, in SST, is catalyzed by a thiosulfate dehydrogenase (TsdA) homolog that has far-higher substrate-affinity than the Sox system of this bacterium, which, remarkably, is also less efficient than the P. pantotrophus Sox. soxB-deletion in SST abolished sulfate-formation from thiosulfate/tetrathionate while thiosulfate-to-tetrathionate conversion remained unperturbed. Physiological studies revealed the involvement of glutathione in SST tetrathionate oxidation. However, zero impact of the knock-out of a thiol dehydrotransferase (thdT) homolog, together with no production of sulfite as an intermediate, indicated that tetrathionate oxidation in SST is mechanistically novel, and distinct from its betaproteobacterial counterpart mediated by glutathione, ThdT, SoxBCD and sulfite:acceptor oxidoreductase. All the present findings collectively highlight extensive functional diversification of sulfur-oxidizing enzymes across phylogenetically close, as well as distant, bacteria.

microbiology↗

bioRxiv2019

RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications.

Brain circuits are composed of vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow highly specific targeting of individual neurons for structural and functional studies, we modified three site-specific DNA recombinases, Cre, Dre and Flp, by combining them with a fungal light-inducible protein, Vivid, so that their recombinase activities can be driven by blue light. We generated viral vectors to express these light-inducible recombinases and demonstrated that they can induce genomic modifications in dense or sparse populations of neurons in live mouse brains controlled by one-photon or two-photon light induction. As an important application, we showed that light-inducible recombinases can produce highly targeted, sparse and strong labeling of individual neurons thereby enabling whole-brain morphological reconstruction to identify their axonal projection specificity. In addition to targeting cortical brain areas, we applied the method in deep targets, with a demonstration of functional calcium imaging. These molecular tools enable spatiotemporally-precise, targeted genomic modifications that will greatly facilitate detailed analysis of neural circuits and linking genetic identity, morphology, connectivity and function.

neuroscience↗

bioRxiv2019

Systematic mapping of drug metabolism by the human gut microbiome

The human gut microbiome harbors hundreds of bacterial species with diverse biochemical capabilities, making it one of natures highest density, highest diversity bioreactors. Several drugs have been previously shown to be directly metabolized by the gut microbiome, but the extent of this phenomenon has not been systematically explored. Here, we develop a systematic screen for mapping the ability of the complex human gut microbiome to biochemically transform small molecules (MDM-Screen), and apply it to a library of 575 clinically used oral drugs. We show that 13% of the analyzed drugs, spanning 28 pharmacological classes, are metabolized by a single microbiome sample. In a proof-of-principle example, we show that microbiome-derived metabolism occurs in vivo, identify the genes responsible for it, and provide a possible link between its consequences and clinically observed features of drug bioavailability and toxicity. Our findings reveal a previously underappreciated role for the gut microbiome in drug metabolism, and provide a comprehensive framework for characterizing this important class of drug-microbiome interactions.

microbiology↗

bioRxiv2019

Cdk1 in germline and the dose of somatic EGFR signaling determine the rate of transit amplification

The division rates of stem cells and their progeny shape the growth and maintenance of tissues. Here, we present a mathematical model that could estimate the stage-wise lifespans of germline stem cells (GSCs) and subsequent transit amplifying (TA) cells from their steady-state distribution in Drosophila testis. Analysis of the wild-type data using this model indicated that the inter-division lifespans of the first two TA cycles remain similar to that of the GSCs, and then reduce by nearly 2-folds for the third and fourth cycles. Also, loss of Cyclin E and Cdk1 functions in the early germline cells, which decreased the rates of GSC divisions, is suggested to extend the lifespans of GSCs and the TA stages without affecting subsequent differentiation. Similar perturbations at the 4 and 8-cell stages, however, arrested the mitoses at the 8-cell stage, and only the Cyclin E-deficient cells continued with premature meiosis. Together, these results suggest that regulation of the G1-S and G2-M transitions in the GSCs and the rapidly dividing TA stages differentially impacts the amplification of the germline pool and subsequent differentiation. The model also helped to quantify distinct influences of these cell cycle regulatory molecules in determining the lifespans at different TA stages.\n\nHighlightsA model for calculating the lifespans of transit amplifying stages from demography. Transit-amplifying divisions accelerate by nearly 2-folds after the second mitosis. Cyclin E and Cdk1 regulate the lifespans of GSCs and transit amplifying cells. The premature arrest of the final transit amplifying division induces meiosis.

developmental biology↗

bioRxiv2018

The integrated stress response mediates type I interferon driven necrosis in Mycobacterium tuberculosis granulomas

Necrosis in the tuberculous granuloma is a hallmark of tuberculosis that enables pathogen survival and transmission. Susceptibility to tuberculosis and several other intracellular bacteria is controlled by a mouse genetic locus, sst1, and mice carrying the sst1-suscepible (sst1S) genotype develop necrotic inflammatory lung lesions, similar to human TB granulomas. Our previous work established that increased disease severity in sst1S mice reflects dysfunctional macrophage effector or tolerance mechanisms, but the molecular mechanisms have remained unclear. Here we demonstrate that sst1S macrophages develop aberrant, biphasic responses to TNF characterized by super-induction of stress and type I interferon pathways after prolonged TNF stimulation with this late-stage response being initiated by oxidative stress and Myc activation and driven via a JNK - IFN{beta} - PKR circuit. This circuit leads to induction of the integrated stress response (ISR) mediated by eIF2 phosphorylation and the subsequent hyper-induction of ATF3 and ISR-target genes Chac1, Trib3, Ddit4. The administration of ISRIB, a small molecule inhibitor of the ISR, blocked the development of necrosis in lung granulomas of M. tuberculosis-infected sst1S mice and concomitantly reduced the bacterial burden revealing that induction of the ISR and the locked-in state of escalating stress driven by type I IFN pathway in sst1S macrophages plays a causal role in the development of necrosis. Our data support a generalizable paradigm in intracellular pathogen-host interactions wherein host susceptibility emerges within inflammatory tissue due to imbalanced macrophage responses to growth, differentiation, activation and stress stimuli. Successful pathogens such as M. tuberculosis may exploit this aberrant response in susceptible hosts to induce necrotic lesions that favor long-term pathogen survival and transmission. Interruption of the aberrant stress response with inhibitors such as ISRIB may offer novel therapeutic strategies.

immunology↗

bioRxiv2018

Chelation therapy using static magnetic field

Static magnetic field (SMF) is reported to mimic chelation agents. In thalassemia blood, SMF minimizes iron overloading effect. In such cells ROS level is reduced, in presence of moderate strength (70mT). Pilot study on transfusion dependent thalassemia, thalassemia carriers and normal red blood clearly indicate the differential effects of SMF on thalassemia, thalassemia carrier and normal cells. SMF also reduces ROS induced DNA damage in lymphocytes. A comparative study on the iron chelating drug deferasirox and SMF treated lymphocytes further confirm our main thesis. This non-invasive therapeutic regime for hemochromatosis may serve the dual purpose of treating, iron overloading and minimizing, cellular damage by lowering the ROS level.

epidemiology↗

bioRxiv2018

Mycobacteria-specific CD4+IFN-γ+ cell expresses naïve-surface markers and confers superior protection against tuberculosis infection compared to central and effector memory CD4+ T cell subsets

Failure of the most recent tuberculosis (TB) vaccine trial to boost BCG mediated anti-TB immunity despite highly durable Th1-specific central (TCM) and effector (TEM) memory cell responses, highlights the importance of identifying optimal T cell targets for protective vaccines. Here we describe a novel, Mycobacterium tuberculosis (Mtb)-specific IFN-{gamma}+CD4+ T cell population expressing surface markers characteristic of naive T cells (TNLM), that were induced in both human (CD45RA+CCR7+CD27+CD95-) and murine (CD62L+CD44-Sca-1+CD122-) systems in response to mycobacteria. In BCG vaccinated subjects and those with latent TB infection, TNLM cells, compared to bonafide naive CD4+ T cells were identified by absence of CD95 expression and had increased expression CCR7 and CD27, the activation markers T-bet, CD69 and PD-1 and the survival marker CD74. Increased TNLM frequencies were noted in the lung and spleen of wild type C57BL6 mice at 2 weeks after infection with Mtb, and progressively decreased at later time points, a pattern not seen in TNF-+CD4+ T cells expressing naive cell surface markers. Importantly, adoptive transfer of highly purified TNLM from vaccinated ESAT-61-20-specific TCR transgenic mice conferred superior protection against Mtb infection in Rag-/- mice when compared with total meory populations (central and effector memory cells). Thus, TNLM cells may represent a memory T cell population that if optimally targeted may significantly improve future TB vaccine responses.

immunology↗

bioRxiv2018

A three year follow-up study of gadolinium enhanced and non-enhanced regions in multiple sclerosis lesions using a multi-compartment T2 relaxometry model

Demyelination, axonal damage and inflammation are critical indicators of the onset and progress of neurodegenerative diseases such as multiple sclerosis (MS) in patients. Due to physical limitations of imaging such as acquisition time and imaging resolution, a voxel in a MR image is heterogeneous in terms of tissue microstructure such as myelin, axons, intra and extra cellular fluids and free water. We present a multi-compartment tissue model which estimates the water fraction (WF) of tissues with short, medium and high T2 relaxation times in a T2 relaxometry MRI voxel. The proposed method is validated on test-retest data of healthy controls. This model was then used to study longitudinal trends of the tissue microstructures for two sub-regions of the lesions: gadolinium enhanced (E+) and non-enhanced (L-) regions of MS lesions in 10 MS patients over a period of three years. The water fraction values in E+ and L- regions were found to be significantly different (p < 0.05) over the period of first three months. The results of this study also showed that the estimates of the proposed T2 relaxometry model on brain tissue microstructures have potential to distinguish between regions undergoing active blood brain barrier breakdown from the other regions of the lesion.

neuroscience↗

bioRxiv2018

The Effect of Productive HPV16 Infection on Global Gene Expression of Cervical Epithelium

Human papillomavirus (HPV) infection is the worlds most common sexually transmitted infection, and is responsible for most cases of cervical cancer. Previous studies of global gene expression changes induced by HPV infection have focused on the cancerous stages of infection, and therefore, not much is known about global gene expression changes at early pre-neoplastic stages of infection. We show for the first time, global gene expression changes of early stage HPV16 infection in cervical tissue using 3-dimensional organotypic raft cultures that produce high levels of progeny virions.\n\ncDNA microarray analysis showed that a total of 594 genes were upregulated and 651 genes were downregulated at least 1.5-fold with HPV16 infection. Gene ontology analysis showed that biological processes including cell cycle progression and DNA metabolism were upregulated, while skin development, immune response, and cell death were downregulated with HPV16 infection in cervical keratinocytes. Individual genes were selected for validation at the transcriptional and translational levels including UBC, which was central to the protein association network of immune response genes, and top downregulated genes RPTN, SERPINB4, KRT23, and KLK8. In particular, KLK8 and SERPINB4 have shown to be upregulated in cancer, which contrasts our results.\n\nOrganotypic raft cultures that allow full progression of the HPV life-cycle have allowed us to identify novel gene modulations and potential therapeutic targets of early stage HPV infection in cervical tissue. Additionally, our results suggest that early stage productive infection and cancerous stages of infection are distinct disease states expressing different transcriptomes.\n\nImportancePersistent HPV infection is responsible for most cases of cervical cancer. Transition from precancerous to cancerous stages of HPV infection is marked by a significant reduction in virus production. Most global gene expression studies of HPV infection have focused on the cancerous stages. Therefore, little is known about global gene expression changes at precancerous stages. For the first time, we measured global gene expression changes at precancerous stages of HPV16 infection in human cervical tissue producing high levels of virus. We identified a group of genes that are typically overexpressed in cancerous stages to be significantly downregulated at the precancerous stage. Moreover, we identified significantly modulated genes that have not yet been studied in the context of HPV infection. Studying the role of these genes in HPV infection will help us understand what drives the transition from precancerous to cancerous stages, and may lead to development of new therapeutic targets.

genomics↗

bioRxiv2018

Controlling insulin resistance through modulation of interplay between mediators of cellular senescence: A mathematical study

Obesity, metabolic syndrome and premature ageing form a hugely researched and discussed area of interest these days. In the pathology of this cluster of conditions, adipose tissue is gaining attention as a major playground for interplay between metabolic stress, inflammation and accelerated ageing, and not merely being an energy storage tank. Drastic elevation in the levels of reactive oxygen species, due to lipid overload and excessive lipolysis, causes genotoxic damage such as shortening of telomeres (an indicator of accelerated cell ageing), increased mRNA and protein expression for p53, p21, TNF-, IL-6 (interleukin 6), impaired insulin mediated glucose uptake, and decreased TERT mRNA expression. The increase of p53 in adipocytes is deleterious, since elevated p53 results in pre-mature ageing of fat tissues which secrete pro-inflammatory cytokines thereby contributing to insulin resistance. But inhibition of p53 as a therapeutic target, as suggested by many previous studies, could result in developing high risks of cancer. The association between hyperlipidemic/hyperglycaemic stress, premature growth arrest and insulin resistance, thus, forms an interesting premise for searching targets and designing interventions for therapy of metabolic syndrome, type 2 diabetes mellitus etc. We developed a mathematical study involving a 5D ODE model, which revealed crucial parametric conditions governing p53 dynamics in the case of metabolic stress-induced cellular senescence, and shed light on potential strategies to reduce pro-inflammatory cytokine levels which exacerbate insulin resistance through premature cellular ageing.\n\nHighlightsO_LIp53 oscillations signify DNA repair, and persistent stress causes prolonged surge in p53 levels inducing cellular senescence.\nC_LIO_LIp53-induced cellular senescence promotes inflammation and enhances progression of insulin resistance.\nC_LIO_LIRegulation of Mdmx and Akt can be a strategy to rejuvenate ageing cells through management of IL-6 dynamics.\nC_LI

systems biology↗

bioRxiv2017

Macrophage resilience and control of intracellular bacteria requires sst1-dependent integration of c-Myc, stress response and type I IFN pathways

Host susceptibility to tuberculosis and several other intracellular bacteria is controlled by a mouse genetic locus, sst1. Necrotic inflammatory lesions, similar to human TB granulomas, are a hallmark of the sst1 susceptible phenotype. Our previous work established that increased disease severity in sst1 susceptible mice reflects dysfunctional macrophage effector or tolerance mechanisms, but the molecular mechanisms have been unclear.\n\nWe demonstrate that sst1-deficient macrophages develop aberrant, biphasic responses to TNF, characterized by super-induction of stress and type I interferon pathways after prolonged TNF stimulation. This late stage response was initiated by oxidative stress and Myc. It was driven via a JNK - IFN{beta} - PKR feed-forward circuit locking the susceptible macrophages in a state of escalating stress. Consequently, prolonged TNF stimulation of the susceptible macrophages reduced their resilience to subsequent infection with intracellular bacteria.\n\nThe data support a generalizable paradigm in host - pathogen interactions, where susceptibility emerges gradually within inflammatory tissue due to imbalanced macrophage responses to growth, differentiation, activation and stress stimuli prior to encountering pathogens. This explains how successful pathogens may locally bypass mechanisms of resistance in otherwise immunocompetent hosts and suggests novel therapeutic strategies.

immunology↗

bioRxiv2017

Antiferromagnetic switch in serum

1.Ferritin contains naturally occurring iron oxide nanoparticle surrounded by a structured spherical array of peptide residues that provides tremendous stability to this iron storage protein. We use synthetic citrate coated Super Paramagnetic Iron Oxide Nanoparticles (SPIONs) and static magnetic field in exploring the Ferritin induced magnetic environment of human serum samples with varying ferritin level collected from thalassemic patients. We report anti-ferromagnetic properties of serum in patients with iron overloading. Magnetic pulling by an external magnetic field showed a cusp-like behavior with increasing concentration of serum Ferritin measured by standard ELISA based kit. A reduction in the extent of pulling after a threshold concentration of Ferritin (1500 ng/ml) suggests a Ferritin dependent magnetic switching.Negative magnetization (anti-ferromagnetization) was confirmed by Vibrating Sample Magnetometric (VSM) analysis of SPION-serum mixture containing very high level of Ferritin. Such magnetic switching may have a possible role in iron homeostasis during overloading of Ferritin.\n\n3. AbbreviationsSPIONs: Super Paramagnetic Iron Oxide Nanoparticles, VSM: Vibrating Sample Magnetometry, SQUID: Super conducting Quantum Interference Device, PCS: Photon Correlation Spectroscopy

biophysics↗

bioRxiv2017

Use of a scoring strategy to determine clinical risk of progression and risk group-specific treatment adherence in subjects with latent tuberculosis infection

BackgroundAnnual incidence of active tuberculosis (TB) cases has plateaued in the US from 2013-2015. Most cases are from reactivation of latent tuberculosis infection (LTBI). A likely contributor is suboptimal LTBI treatment completion rates in subjects at high risk of developing active TB. It is unknown whether these patients are adequately identified and treated under current standard of care.\n\nMethodsIn this study, we sought to retrospectively assess the utility of an online risk calculator (tstin3d.com) in determining probability of LTBI and defining the characteristics and treatment outcomes of Low: 0-<10%, Intermediate: 10-<50% and High: 50-100% risk groups of asymptomatic subjects with LTBI seen between 2010-2015.\n\nResults51(41%), 46 (37%) and 28 (22%) subjects were in Low, Intermediate and High risk groups respectively. Tstin3d.com was useful in determining the probability of LTBI in tuberculin skin test positive US born subjects. Of 114 subjects with available treatment information, overall completion rate was 61% and rates of completion in Low (60%), Intermediate (63%) and High (57%) risk groups were equivalent. 75% subjects in the 3HP group completed treatment compared to 58% in the INH group. Provider documentation of important clinical risk factors was often incomplete. Logistic regression analysis showed no clear trends of treatment completion being associated with assessment of a risk factor.\n\nConclusionThese findings suggest tstin3d.com could be utilized in the US setting for risk stratification of patients with LTBI and select treatment based on risk. Current standard of care practice leads to subjects in all groups finishing treatment at equivalent rates.

epidemiology↗