Biology subjects

Bhattacharya, P.

Publications and source records attributed to Bhattacharya, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Two-State Effective Connectivity Predicts the effect of Anterior Cingulate Cortex Excitatory / Inhibitory Balance on Posterior Cingulate Cortex

Aims Excitatory/inhibitory imbalance - the equilibrium between glutamatergic excitation and {gamma}-Aminobutyric acid (GABA)ergic inhibition - is implicated in psychosis and may precede psychosis onset. Methods To investigate whether excitatory/inhibitory balance relates to subclinical psychotic experiences, anxiety and depression, we developed a network-level measure integrating Magnetic Resonance Spectroscopy Glutamate/GABA ratios with effective connectivity during resting-state fMRI. In 20 healthy young adults (aged between 18-32; 50% female), we first measured excitatory/inhibitory balance, operationalised as Glutamate/GABA and Glutamate+Glutamine(Glx)/GABA ratio, in the dorsal anterior cingulate cortex. Second, we applied Two-state Dynamic Causal Modelling to assess effective connectivity of the default-mode network, using these ratios as empirical priors to determine how they translate into network connectivity. Third, we ran Bayesian Model Selection at the model and family levels to identify the optimal models. Results The two-state model with Glx/GABA ratio as direct input into the posterior cingulate cortex best explained the data. This best-fitting model incorporated the neurometabolite ratio with Glutamate and GABA and used two-state connectivity. Conclusions Excitatory/inhibitory balance underlies resting-state effective connectivity, with the Glx/GABA ratio shaping connectivity networks. This pathway highlights excitatory/inhibitory balance as a predictor of two-state brain networks, potentially aiding identification of high-risk individuals and informing new interventions.

neuroscience↗

bioRxiv2026

Influenza virus Non Structural protein 1 (NS1) Chaperones Nucleoprotein (NP) Oligomerization to Coordinate Ribonucleoprotein Assembly and Genome Replication

Influenza virus nucleoprotein (NP) co-transcriptionally enwraps viral genomic/antigenomic RNAs to assemble viral ribonucleoprotein complexes (RNPs), while the non-structural protein-1 (NS1) is classically recognized as an antagonist of host antiviral responses. Although NP-NS1 interaction has long been reported, the molecular basis of this protein-protein interaction and its relevance in the virus life cycle remain elusive. Here, we define the NP-NS1 interaction interface and uncover a noncanonical role of NS1 in regulating RNP assembly and viral genome replication. Using integrated biochemical, biophysical, and structural analyses, we demonstrate that the RNA-binding domain (RBD) of NS1 directly engages the NP tail-loop, conferring high affinity for monomeric NP. Functional assays reveal that a cytoplasm-restricted NS1 variant acts as an NP-specific chaperone by stabilizing monomeric NP through sequestration of its intrinsically flexible tail-loop and by scaffolding NP-NP interactions. During influenza virus infection, phosphorylation at the homotypic interface restricts NP in a replication-competent monomeric state. Cytoplasmic NS1 recruits these phosphorylated monomeric NPs into assembling RNPs, thereby facilitating viral genome replication and virus propagation. Collectively, our findings establish NS1 as a selective cytoplasmic chaperone of NP and reveal a novel regulatory axis governing influenza virus RNP biogenesis and replication.

molecular biology↗

bioRxiv2025

Intraepithelial lymphocytes exhibit selective immunity to intestinal pathogens

Intraepithelial lymphocytes (IEL) are abundant, tissue-resident T cells critical for intestinal immune surveillance, yet their precise roles have remained elusive due to the lack of models enabling their selective genetic ablation. Here, we report the generation of Gzmb-Cre knock-in mice, that when crossed with inducible Diphtheria toxin receptor mice, allows targeted and inducible ablation of IELs without perturbing peripheral immunity. Using this model (referred to as IELiDTR), we demonstrate that IELs are dispensable for intestinal homeostasis, including epithelial architecture, barrier function and microbial composition. However, loss of IELs led to increased intestinal infection by Salmonella Typhimurium and Cryptosporidium parvum, but did not affect responses to Listeria monocytogenes infection or DSS colitis. Interestingly, IEL deficiency reduced fecundity of the intestinal nematode, Heligmosomoides polygyrus, despite unaltered worm burden, suggesting a permissive role in helminth colonization. These findings position IELs as evolutionary-tuned sentinels against co-evolved pathogens that can cause lethal diarrheal diseases, and establish the IELiDTR mouse as a vital genetic tool for dissecting IEL function in host-pathogen interactions in vivo.

immunology↗

bioRxiv2025

Targeted Molecular MRI of Colorectal Cancer by Antibody Functionalized Hyperpolarized Silicon Particles

The development of non-invasive, non-ionizing sensitive molecular targeting approaches to detect colorectal cancer (CRC) lesions is warranted to improve high risk patient outcomes. Hyperpolarized silicon nanoparticles and microparticles are potentially well-suited to act as targeted molecular imaging agents because of their overall biocompatibility and long-lasting enhanced magnetic resonance imaging (MRI) signals. In this study, dynamic nuclear polarization was performed on silicon particles functionalized with an antibody to Mucin-1 (MUC1), a surface mucin glycoprotein aberrantly expressed in CRC. Antibody conjugation to the particle surface did not affect 29Si hyperpolarization characteristics. Similarly, conjugation and the dynamic nuclear polarization process did not adversely affect the affinity of the targeting antibody. In vivo MRI scans performed 10-15 minutes after luminal administration of targeted hyperpolarized particles into human MUC1-expressing orthotopic CRC mouse models showed that particles actively targeted tumor sites. These results were supported by chemical and biological controls and blocking experiments as well as correlative immunohistochemical analysis. These surface-functionalized silicon particles are under development as a platform technology that will allow non-invasive molecular targeting of CRC using hyperpolarized MRI. Single Sentence SummaryTargeted molecular MR imaging of colorectal cancer by hyperpolarized silicon particles functionalized with mucin 1 antibody.

cancer biology↗

bioRxiv2024

Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis

Immune checkpoint inhibition (ICI) has emerged as a critical treatment strategy for squamous cell carcinoma of the head and neck (HNSCC) that halts the immune escape of the tumor cells. Increasing evidence suggests that the onset, progression, and lack of/no response of HNSCC to ICI are emergent properties arising from the interactions within the tumor microenvironment (TME). Deciphering how the diversity of cellular and molecular interactions leads to distinct HNSCC TME subtypes subsequently governing the ICI response remains largely unexplored. We developed a cellular-molecular model of the HNSCC TME that incorporates multiple cell types, cellular states, and transitions, and molecularly mediated paracrine interactions. An exhaustive simulation of the HNSCC TME network shows that distinct mechanistic balances within the TME give rise to the five clinically observed TME subtypes such as immune/non-fibrotic, immune/fibrotic, fibrotic only and immune/fibrotic desert. We predict that the cancer-associated fibroblast, beyond a critical proliferation rate, drastically worsens the ICI response by hampering the accessibility of the CD8+ killer T cells to the tumor cells. Our analysis reveals that while an Interleukin-2 (IL-2) + ICI combination therapy may improve response in the immune desert scenario, Osteopontin (OPN) and Leukemia Inhibition Factor (LIF) knockout with ICI yields the best response in a fibro-dominated scenario. Further, we predict Interleukin-8 (IL-8), and lactate can serve as crucial biomarkers for ICI-resistant HNSCC phenotypes. Overall, we provide an integrated quantitative framework that explains a wide range of TME-mediated resistance mechanisms for HNSCC and predicts TME subtype-specific targets that can lead to an improved ICI outcome.

cancer biology↗

bioRxiv2024

From tumor microenvironment to immuno-therapeutic outcomes for solid tumors: A systems theoretic approach

Increasing evidence suggests the tumor microenvironment (TME) governs solid tumor response to immune checkpoint inhibition (ICI). Decoding the relationship between the cell compositional diversity of the tumor microenvironment (TME) and the therapeutic outcomes has been a longstanding problem in solid tumor research. In this work, we develop a systems-theoretic formalism to decipher the key mechanisms of growth, proliferation, immune evasion, and drug resistance that run common across solid tumors in the context of Immune Checkpoint Inhibitors (ICI). We reconstructed a core TME network in common across most solid tumors, containing multiple tumor and non-tumor cell types in distinct functional states, and molecular agents mediating cellular signaling and cell-cell interactions. Our analysis shows that the core TME network is sufficient to yield a multiplicity of attractors corresponding to clinically observed TME subtypes namely, immune or fibro dominated, immune or fibro desert, and immune and fibro deficient. Importantly, the reachability around the pre-ICI attractors governs the response to ICI explaining the TME subtype-specific therapy outcomes. We analyzed the attractor transition network to identify subtype-specific combination therapies that can drive unresponsive TME to a responsive subtype. We derived mathematical conditions relating TME balances to determine the limits of the efficacy of combination therapies. Our results hold for a large class of smooth biochemical kinetics with monotone and bounded interactions and (semi-)concave proliferation rules. The analytical findings have been verified with extensive simulation of different TME sub-types. Overall, we propose a generalized systems formalism that accounts for the TME properties governing ICI response and can aid in designing intervention strategies for improved tumor prognosis. Significance StatementNon-responsive therapy outcomes have been a persistent problem in cancer treatment. Predicting the possibility of non-responsiveness to a particular therapy from the pre-treatment composition of the tumor microenvironment (TME) aids in designing appropriate combination treatment strategies toward an improved prognosis. The present work develops a systems-theoretic formalism that aims to unfold the mechanisms behind solid tumors growth, non-responsiveness, and recurrence. Unlike a single model, the proposed formalism does not assume any particular kinetics, barring some minimal assumptions. This enables us to explain some of the relevant observations made by the recent experimental studies. Finally, the closed-form conditions obtained for responsivity and recurrence can also guide novel therapeutic strategies that may be able to restore responsiveness to immunotherapy.

systems biology↗

bioRxiv2024

Metabolic Reprogramming by Mutant GNAS Creates an Actionable Dependency in Intraductal Papillary Mucinous Neoplasms of the Pancreas

ObjectiveOncogenic "hotspot" mutations of KRAS and GNAS are two major driver alterations in Intraductal Papillary Mucinous Neoplasms (IPMNs), which are bona fide precursors to pancreatic ductal adenocarcinoma. We previously reported that pancreas-specific KrasG12D and GnasR201C co-expression in p48Cre; KrasLSL-G12D; Rosa26LSL-rtTA; Tg (TetO-GnasR201C) mice ("Kras;Gnas" mice) caused development of cystic lesions recapitulating IPMNs. Here, we aim to unveil the consequences of mutant GnasR201C expression on phenotype, transcriptomic profile, and genomic dependencies. DesignWe performed multimodal transcriptional profiling (bulk RNA sequencing, single cell RNA sequencing, and spatial transcriptomics) in the "Kras;Gnas" autochthonous model and tumor-derived cell lines (Kras;Gnas cells), where GnasR201C expression is inducible. A genome-wide CRISPR/Cas9 screen was conducted to identify potential vulnerabilities in KrasG12D;GnasR201Cco-expressing cells. ResultsInduction of GnasR201C - and resulting G(s)alpha signaling - leads to the emergence of a gene signature of gastric (pyloric type) metaplasia in pancreatic neoplastic epithelial cells. CRISPR screening identified the synthetic essentiality of glycolysis-related genes Gpi1 and Slc2a1 in KrasG12D;GnasR201C co-expressing cells. Real-time metabolic analyses in Kras;Gnas cells and autochthonous Kras;Gnas model confirmed enhanced glycolysis upon GnasR201C induction. Induction of GnasR201C made KrasG12D expressing cells more dependent on glycolysis for their survival. Protein kinase A-dependent phosphorylation of the glycolytic intermediate enzyme PFKFB3 was a driver of increased glycolysis upon GnasR201C induction. ConclusionMultiple orthogonal approaches demonstrate that KrasG12D and GnasR201C co-expression results in a gene signature of gastric pyloric metaplasia and glycolytic dependency during IPMN pathogenesis. The observed metabolic reprogramming may provide a potential target for therapeutics and interception of IPMNs. SUMMARYO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIActivating "hotspot" mutations of KRAS and GNAS are found in a majority of Intraductal Papillary Mucinous Neoplasms (IPMNs). C_LIO_LIExpression of mutant KRAS and GNAS drives development of IPMN-like cystic lesions in the murine pancreas that eventually progress to pancreatic ductal adenocarcinoma (PDAC). C_LI What this study addsO_LIMutant GNAS and the resulting aberrant G(s)alpha signaling drives a transcriptional signature of gastric (pyloric type) metaplasia in IPMNs with mucin production. C_LIO_LIAberrant G(s)alpha signaling enhances glycolysis via protein kinase A-dependent phosphorylation of the glycolytic enzyme PFKFB3. C_LIO_LIEnhanced glycolysis in KRAS;GNAS-mutated IPMN cells is validated via multiple orthogonal approaches in vitro and in vivo and represents an actionable metabolic vulnerability. C_LI How this study might affect research, practice or policyO_LIThe present study provides mechanistic insight into how aberrant G(s)alpha signaling alters the biology of Kras-mutant pancreatic epithelial neoplasia through metaplastic and metabolic reprogramming. C_LIO_LITargeting glycolysis in IPMNs may represent both a therapeutic avenue as well as an opportunity for intercepting progression to invasive cancer. C_LI

cancer biology↗

bioRxiv2022

Design principles for perfect adaptation in biological networks with nonlinear dynamics

Establishing a mapping between the emergent biological properties and the repository of network structures has been of great relevance in systems and synthetic biology. Adaptation is one such biological property of paramount importance that promotes regulation in the presence of environmental disturbances. This paper presents a nonlinear systems theory-driven framework to identify the design principles for perfect adaptation. Based on the prior information about the network, we frame precise mathematical conditions for adaptation using nonlinear systems theory. We first deduce the mathematical conditions for perfect adaptation for constant input disturbances. Subsequently, we first translate these conditions to specific necessary structural requirements for adaptation in networks of small size and then extend to argue that there exist only two classes of architectures for a network of any size that can provide local adaptation in the entire state space, namely, incoherent feed-forward structure and negative feedback loop with buffer node. The additional positiveness constraints further narrow the admissible set of network structures. This also aids in establishing the global asymptotic stability for the steady state given a constant input disturbance. The entire method does not assume any explicit knowledge of the underlying rate kinetics, barring some minimal assumptions. Finally, we also discuss the infeasibility of the incoherent feed-forward networks (IFFLP) to provide adaptation in the presence of downstream connections. Detailed and extensive simulation studies corroborate the theoretical findings. Moreover, we propose a generic and novel algorithm based on a nonlinear systems theory to unravel the design principles for global adaptation.

systems biology↗

bioRxiv2022

On biological networks capable of robust adaptation in the presence of uncertainties: A systems-theoretic approach

Biological adaptation, the tendency of every living organism to regulate its essential activities in environmental fluctuations, is a well-studied functionality in systems and synthetic biology. In this work, we present a generic methodology inspired by systems theory to discover the design principles for robust adaptation, perfect and imperfect, in two different contexts: (1) in the presence of deterministic external disturbance and (2) in a stochastic setting. In all the cases, firstly, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as design requirements for the underlying networks. Thus, contrary to the existing approaches, the proposed methodologies provide an exhaustive set of admissible network structures without resorting to computationally burdensome brute-force techniques. Further, the proposed frameworks do not assume prior knowledge about the particular rate kinetics, thereby validating the conclusions for a large class of biological networks. In the deterministic setting, we show that unlike the incoherent feed-forward network structures (IFFLP), the modules containing negative feedback with buffer action (NFBLB) are robust to parametric fluctuations when a specific part of the network is assumed to remain unaffected. To this end, we propose a sufficient condition for imperfect adaptation and show that adding negative feedback in an IFFLP topology improves the robustness concerning parametric fluctuations. Further, we propose a stricter set of necessary conditions for imperfect adaptation. Turning to the stochastic scenario, we adopt a Wiener-Kolmogorov filter strategy to tune the parameters of a given network structure towards minimum output variance. We show that both NFBLB and IFFLP can be used as a reduced order W-K filter. Further, we define the notion of nearest neighboring motifs to compare the output variances across different network structures. We argue that the NFBLB achieves adaptation at the cost of a variance higher than its nearest neighboring motifs whereas the IFFLP topology produces locally minimum variance while compared with its nearest neighboring motifs. We present numerical simulations to support the theoretical results. Overall, our results present a generic, systematic, and robust framework for advancing the understanding of complex biological networks.

systems biology↗

bioRxiv2022

Leishmania major centrin knock-out parasites alter the Kynurenine- aryl hydrocarbon receptor signaling to produce a pro-inflammatory response

Leishmaniasis is a parasitic disease that is prevalent in approximately 88 countries, and yet no licensed human vaccine exists against it. Towards control of leishmaniasis, we have developed Leishmania major centrin gene deletion mutant strains (LmCen-/-) as a live attenuated vaccine, which induces a strong Th1 response to provide IFN-{gamma}-mediated protection to the host. However, the immune mechanisms of such protection remain to be understood. Metabolomic reprogramming of the host cells following Leishmania-infection has been shown to play a critical role in pathogenicity and shaping the immune response following infection. Here, we applied untargeted mass spectrometric analysis to study the metabolic changes induced by infection with LmCen-/- and compared those with virulent L. major parasite infection to identify the immune mechanism of protection. Our data shows that immunization with LmCen-/- parasites, in contrast to virulent L. major infection, alters tryptophan metabolism to down-regulate kynurenine-AhR signaling and promote a pro-inflammatory response.

systems biology↗

bioRxiv2022

Dual scRNA-Seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

Although phagocytic cells are documented targets of Leishmania parasites, it is unclear whether these parasites can infect other cell types. In this study, we describe a computational approach that exploits scRNA-seq to simultaneously analyze the transcriptomic signatures of the host cell and to identify rare and uncommon cells that harbor Leishmania donovani in the spleen and bone marrow. Individual cells were annotated as parasitized based on the presence of L. donovani transcripts that were detected with high accuracy. This unbiased approach allowed identification of heterogenous parasitized cell populations that cannot be detected by conventional methods. Consistent with previous studies, analysis of spleen cells isolated from L. donovani infected mice revealed inflammatory monocytes as the dominant parasitized cells. In addition, megakaryocytes, basophils, and NK cells were found to be the rare cells infected in the spleen. Unexpectedly, hematopoietic stem cells (HSCs), not known to be phagocytic, were the dominant cells parasitized cell in the bone marrow. In addition, eosinophils, megakaryocytes, and basal cells were the rare bone marrow cells found to be infected. scRNA-seq analysis revealed known phagocytic receptors Fc{gamma}R and CD93 are expressed on HSCs. In vitro studies using purified HSCs showed that these cells can phagocytize L. donovani. Parasitized HSCs were also detectable in the bone marrow of mouse infected with L donovani.. This unbiased dual scRNA-seq approach enables identification of rare and uncommon parasitized cells that could be involved in pathogenesis, persistence, and protective immunity. Further, such approach could be used to study pathogenesis of other infectious agents.

immunology↗

bioRxiv2021

Skin resident memory cells generated by the L. major centrin gene deleted parasites mediate protective immune response analogous to leishmanization

Leishmaniasis is a vector-borne parasitic disease transmitted through the bite of a sand fly with no available vaccine for humans. Recently, we have developed a live attenuated Leishmania major centrin gene deleted parasite strain (LmCen-/-) that induced protection against a homologous and heterologous challenges. The protection is mediated by IFN{gamma} secreting CD4+ T effector cells and multifunctional T cells, which is analogous to leishmanization. Previously, skin tissue resident memory T cells (TRM cells) were shown to be crucial for host protection in a leishmanization model. In this study, we evaluated generation and function of skin TRM cells following immunization with LmCen-/- parasites and compared those with leishmanization. In the absence of recoverable LmCen-/- parasites, the skin of immunized mice showed functional TRM cells comparable to leishmanized mice. The generation of the skin TRM cells was supported by the induction of cytokines and chemokines essential for their production and survival. Following challenge infection with wild type L. major, TRM cells specific to L. major were rapidly recruited and proliferated at the site of infection in the immunized mice which was similar to leishmanization. Further, upon challenge, CD4+ TRM cells induced higher levels of IFN{gamma} and Granzyme B in the immunized and leishmanized mice than non-immunized mice. Taken together, our studies demonstrate that a genetically modified live attenuated Leishmania vaccine generates functional CD4+ TRM cells that mediate protection and can be a safer alternative to leishmanization.

immunology↗

bioRxiv2021

HIV-1 Induction of Tolerogenic DCs is Mediated by Cellular Interaction with Suppressive T Cells

HIV-1 infection gives rise to a multilayered immune impairment in most infected individuals. The crosstalk between Dendritic cells and T cells plays an important part in the induction of immune responses. The chronic presence of human immunodeficiency virus (HIV)-1 during the dendritic cells (DCs) priming and activation of T cells promotes the expansion of suppressor cells in a contact dependent manner. The mechanism behind the T cell side of this HIV induced impairment is well studied, whereas little is known about the reverse effects exerted on the DCs in this setting. Here we assessed the phenotype and transcriptome profile of mature DCs that have been in contact with suppressive T cells. The DCs in the HIV exposed DC-T cell coculture obtained a more tolerogenic/suppressive phenotype with increased expression of e.g., PDL1, Gal-9, HVEM, and B7H3, mediated by their cellular interaction with T cells. The transcriptomic analysis showed a clear type I IFN response profile as well as an activation of pathways involved in T cell exhaustion. Taken together, our data indicate that the prolonged and strong IFN type I signaling induced by the presence of HIV during DC-T cell cross talk could play an important role in the induction of the tolerogenic DCs and suppressed immune response.

immunology↗

bioRxiv2021

A generic systems-theoretic approach to identify biological networks capable of adaptation

Constructing biological networks capable of performing specific biological functionalities has been of sustained interest in synthetic biology. Adaptation is one such ubiquitous functional property, which enables every living organism to sense a change in its surroundings and return to its operating condition prior to the disturbance. In this paper, we present a generic systems theory-driven method for designing adaptive protein networks. First, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as design requirements for the underlying networks. We go on to prove that a protein network with different input-output nodes (proteins) needs to be at least of third-order in order to provide adaptation. Next, we show that the necessary design principles obtained for a three-node network in adaptation consist of negative feedback or a feed-forward realization. Interestingly, the design principles obtained by the proposed method remain the same for a network of arbitrary size and connectivity. Finally, we prove that the motifs discovered for adaptation are non-retroactive for a canonical downstream connection. This result explains how complex biological networks achieve robustness while keeping the core motifs unchanged in the context of a particular functionality. We corroborate our theoretical results with detailed and thorough numerical simulations. Overall, our results present a generic, systematic and robust framework for designing various kinds of biological networks.

systems biology↗

bioRxiv2021

Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits

Cotton fiber development is still an intriguing question to understand the fiber commitment and development. Here, we remapped >350 publicly available cotton RNA sequencing data on recently published cotton genome with [~]400 fold coverage. The differentially expressed genes were clustered in six modules whose functions are specific to commitment, initiation, elongation and Secondary Cell Wall (SCW) fiber development stages. Gene Ontology analysis of commitment and initiation specific modules suggests enrichment of genes involved in organ development. The modules specific for elongation and SCW showed significant enrichment of hydroxyproline-rich proteins and hydrolases. Transcription factors (TFs) binding frequency of defined modules suggested that homeodomain, MYB and NAC expresses at commitment stages but their expression was governed by other TFs. We also mined the stage-specific transcriptional biomarker and Exclusively Expressed Transcripts (EETs) for fiber. These EETs were positively selected during fiber evolution and cotton domestication. The extensive expression profiling of six EETs in 100 cotton genotypes at different fiber developmental stages using nCounter assay and their correlation with eight fiber-related suggests that several EETs are correlated with different fiber quality-related traits. Thus, our study reveals several important genes and pathways that may be important for cotton fiber development and future improvement of cotton.

plant biology↗

bioRxiv2020

Preclinical validation of a second generation leishmanization vaccine against vector transmitted fatal visceral leishmaniasis

Visceral Leishmaniasis (VL) is fatal if untreated. There is no licensed vaccine available against human leishmaniasis. We recently demonstrated protection in mice against L. major infection using a CRISPR genome edited attenuated Leishmania major strain (LmCen-/-). Here, as a pre-clinical step, we evaluated the protective efficacy of LmCen-/- against VL induced by sand fly transmitted Leishmania donovani in hamsters. Intradermal immunization of hamsters with LmCen-/- did not develop any lesion; while still priming a pro-inflammatory immune response. When challenged with L. donovani either by intradermal needle injection or by infected sand flies, LmCen-/--immunized hamsters were protected, not showing spleen or liver pathology averting VL fatality compared to control animals. Spleen cells from LmCen-/- immunized and infected sand fly challenged hamsters produced significantly higher Th1-associated cytokines and chemokines including IFN-{gamma} and TNF-, and significantly reduced expression of the anti-inflammatory cytokines IL-10 and IL-21, compared to non-immunized challenged animals. We further developed a GLP-grade LmCen-/- which showed equal protection as laboratory-grade LmCen-/- parasites in hamsters. Importantly, GLP-grade LmCen-/- parasites also induced a proinflammatory immune response in the PBMCs isolated from healthy people living in non-endemic and endemic for VL as well as cured VL people living in endemic region. Together, this study demonstrates that the LmCen-/- parasites are safe and efficacious against VL and it is a strong candidate vaccine to be tested in a human clinical trial.

immunology↗

bioRxiv2020

Soil bacterial community diversity and composition vary more with elevation than seasons in alpine habitats of western Himalaya

Soil heterotrophic respiration-driven CO2 emissions, its impact on global warming and the mechanistic roles of soil bacterial communities in this process have been an area of active research. However, our knowledge regarding the effects of environmental changes on soil bacterial communities is limited. To this end, the climate-sensitive high-altitude alpine ecosystems offer ideal opportunities to investigate relationship between climate change and bacterial communities. While data from several high-altitude mountain regions suggest that local environment factors and geological patterns govern bacterial communities, no information is available from the Himalaya. Here we provide baseline information on seasonal soil bacterial community diversity and composition along a 3200-4000 m elevation gradient covering four alpine habitats (subalpine forest, alpine scrub, alpine meadow and moraine) in Gangotri National Park, western Himalaya. Bacterial metabarcoding data from 36 field-collected samples showed no elevation trend in the bacterial richness and a non-monotonous decrease in their diversity. Further, their community diversity and composition varied significantly among habitats along elevation but were stable seasonally within each habitat. The richness was primarily influenced by soil inorganic carbon (SOC) and total nitrogen (TN), whereas temperature, SOC and TN affected diversity and composition patterns. Given the importance of the Himalaya in the context of global carbon cycle this information will help in accurate modeling of climate adaptation scenarios of bacterial niches and their downstream impacts towards climate warming.

genomics↗

bioRxiv2020

Hypercholesterolemia Impairs Clearance of Extracellular DNA and Promotes Inflammation and Atherosclerotic Plaque Progression

Defects in clearance of extracellular DNA due to sub-optimal activity of DNase results in exacerbated inflammation and contributes to the pathophysiology of atherosclerosis and other inflammatory diseases. However, the physiological mechanisms that regulate systemic DNase levels and the basis of its functional impairment during disease are poorly understood. Using a mouse model of experimental increase in systemic extracellular DNA levels, we identify the existence of a physiologic DNA-induced DNase response. Importantly, hypercholesterolemia in mice impairs this critical DNA-induced DNase response through an endoplasmic reticulum stress-mediated mechanism with consequences in advanced atherosclerotic plaque progression including increased extracellular DNA accumulation, exacerbated inflammation, and development of pathological features of necrotic rupture-prone vulnerable plaques. From a translational standpoint in humans, we demonstrate that individuals with hypercholesterolemia have elevated systemic extracellular DNA levels and decreased plasma DNase activity. These data suggest that the restoration of DNA-induced DNase response could be a potential therapeutic strategy to promote inflammation resolution during hypercholesterolemia.

immunology↗