Biology subjects

Saha, B.

Publications and source records attributed to Saha, B..

17 recordsLinked to original sources

bioRxiv2026

Screening of Potential Vaccine Candidate and Sera Based Diagnostic Markers from N-linked Surface Glycoproteins of Entamoeba histolytica

Pathogenesis inflicted by Entamoeba histolytica causes amoebic diarrhea and liver abscesses and is one of the leading causes of mortality from parasitic disease worldwide. Preventive therapeutics in the form of a vaccine could be highly effective at providing umbrella protection for a vulnerable community. In this study, a group of ten putative hypothetical surface N-linked glycoproteins was examined to assess their potential as vaccine candidates and/or diagnostic markers against amoebic intestinal colitis and liver abscesses. To evaluate the immunogenicity of putative surface glycoproteins, we used Entamoeba histolytica-infected patients sera from Bangladesh and then assessed the titer of antibody these glycoproteins elicited in patients by enzyme-linked immunosorbent assay (ELISA) and immunoblot. Based on this study, eight of ten surface glycoproteins were found immunogenic, as specific antibodies against these glycoproteins were detected in patients sera. Three of the immunogenic glycoproteins showed strong IgG antibody responses in both patients with intestinal amoebiasis and those with liver abscess. On the other hand, the other two glycoproteins showed the presence of specific serum antibodies exclusively in patients with amoebic liver abscesses, not in individuals with amoebic colitis. The remaining two glycoproteins showed more specific sera antibodies against ALA, but the preference was not very distinct. Immunolocalization with a specific antibody against the most immunogenic glycoproteins further confirmed their presence in the cell membrane. This differential immunogenicity of these glycoproteins in the two groups of patients qualifies them to become prospective sera-based diagnostic markers and also has the potential to become vaccine candidates for amoebiasis protection.

immunology↗

bioRxiv2025

A role for CASM in the repair of damaged Golgi architecture

The term CASM describes a process in which MAP1LC3B/LC3B and other Atg8-family proteins are covalently ligated to lipids in damaged endomembranes. While CASM is commonly described as a cytoprotective response to multiple types of membrane damage, how CASM helps cells maintain homeostasis is still unclear. Here, we show that CASM maintains Golgi apparatus architecture following the loss of TRIM46, a ubiquitin ligase with roles in microtubule organization. TRIM46 deficient cells were notable for enhanced TFEB-driven lysosomal biogenesis and Golgi ribbon fragmentation, with colocalization of the trans-Golgi marker TGOLN2 and the Atg8-family proteins LC3B and GABARAP. Further studies revealed that the Golgi Atg8ylation seen in TRIM46 knockout cells was not degradative and mechanistically resembled CASM. Genetic inhibition of CASM in TRIM46 deficient cells reduced TFEB activation and exacerbated the Golgi morphology defects, suggesting that CASM contributes to Golgi repair. Accordingly, Golgi reformation after drug-induced fragmentation was impaired upon knockdown of CASM genes. Together, these studies identify lysosomal biogenesis and CASM as coordinated features of a Golgi damage response, with CASM acting to preserve Golgi integrity.

cell biology↗

bioRxiv2025

Measuring morphogen transport over multiple spatial scales in live zebrafish embryos

Morphogenesis is controlled by signalling morphogens that form gradients across the embryo. The gradient formation requires that the low molecular weight morphogens slow down their diffusion by at least one order of magnitude. However, the precise slow-down of diffusion across the relevant micrometre scales has not been directly observed. Here, we develop and employ Single-Plane Illumination Microscope based spatial Fluorescence Cross-Correlation Spectroscopy (SPIM-sFCCS) to directly measure the diffusion coefficient of the morphogen Squint in early zebrafish embryos as a function of topography and length scale. We show that Squints diffusion coefficient changes on length scales that are commensurate with the diameter of the intercellular spaces in the embryo and that the slow-down is regulated by receptor binding. The slowdown can be reduced by either the knockdown of Activin receptor 2b, a receptor for Squint, or the overexpression of Lefty2, an inhibitor of Squint. Based on our results and supporting simulations, we propose an interstitial space-dependent transient receptor binding and diffusing mechanism to explain this slowdown, which is crucial for gradient formation and embryonic patterning.

developmental biology↗

bioRxiv2024

BMP signalling attenuates intercellular adhesion to drive mesenchyme migration during fin fold morphogenesis

The development of the vertebrate limb bud is a multifactorial process involving the coordinated activity of diverse signalling pathways and cell types. BMP signalling has been consistently shown to play an integral role during the patterning of mouse and chick limbs. However, the molecular mechanisms and cellular processes underlying its contribution to limb development are poorly understood. Using zebrafish embryos, we demonstrate a novel role of BMPs in driving median fin fold morphogenesis, an evolutionary related structure. Our findings indicated that a graded BMP signal is established in the emerging fin fold along the proximo-distal axis, with the fin mesenchymal cells being identified as the primary target of the signalling cue. Pharmacological and genetic ablation of BMP signalling in the fin fold inhibited the normal migration of the mesenchymal cells into the fin fold. The observed inhibition of migration was accompanied by the elongation in mesenchymal cell shape, which hinted at the possibility of altered physical forces acting on the cell population. We observed that loss of BMP signalling led to the cellular re-distribution and altered membrane dynamics of N-cadherin in the fin mesenchymal cells, which manifested as an increase in homotypic cell adhesion. This change in cell-adhesion serves as the mechanistic basis for the observed defect in migration. Furthermore, inability to detach due to loss of BMP signalling occurs independently of sphingosine-1-phosphate signalling that generates a gradient of mesenchyme adhesion to the underlying matrix. Overall, this study highlights the cellular and molecular mechanism underlying the role of BMPs in coordinating early fin bud morphogenesis.

developmental biology↗

bioRxiv2024

Coordinated Regulation of Renal Glucose Reabsorption and Gluconeogenesis by mTORC2 and Potassium

BackgroundThe kidney proximal tubule is uniquely responsible for reabsorption of filtered glucose and gluconeogenesis (GNG). Insulin stimulates glucose transport and suppresses GNG in the proximal tubule, however, the signaling mechanisms and coordinated regulation of these processes remain poorly understood. The kinase complex mTORC2 is critical for regulation of growth, metabolism, solute transport, and electrolyte homeostasis in response to a wide array of inputs. Here we examined its role in the regulation of renal glucose reabsorption and GNG. MethodsRictor, an essential component of mTORC2, was knocked out using the Pax8-LC1 system to generate inducible tubule specific Rictor knockout (TRKO) mice. These animals were subjected to fasting, refeeding, and variation in dietary K+. Metabolic parameters including glucose homeostasis and renal function were assessed in balance cages. Kidneys and livers were also harvested for molecular analysis of gluconeogenic enzymes, mTORC2-regulated targets, and plasma membrane glucose transporters. ResultsOn a normal chow diet, TRKO mice had marked glycosuria despite indistinguishable blood glucose relative to WT controls. Kidney plasma membrane showed lower SGLT2 and SGLT1 in the fed state, supporting reduced renal glucose reabsorption. Additional metabolic testing provided evidence for renal insulin resistance with elevated fasting insulin, impaired pyruvate tolerance, elevated hemoglobin A1c, and increased renal gluconeogenic enzymes in the fasted and fed states. These effects were correlated with reduced downstream phosphorylation of Akt and the transcription factor FOXO4, identifying a novel role of FOXO4 in the kidney. Interestingly, high dietary K+ prevented glycosuria and excessive GNG in TRKO mice, despite persistent reduction in mTORC2 substrate phosphorylation. ConclusionRenal tubule mTORC2 is critical for coordinated regulation of sodium-glucose cotransport by SGLT2 and SGLT1 as well as renal GNG. Dietary K+ promotes glucose reabsorption and suppresses GNG independently of insulin signaling and mTORC2, potentially providing an alternative signaling mechanism in states of insulin resistance. SIGNIFICANCE STATEMENTThe kidney contributes to regulation of blood glucose through reabsorption of filtered glucose and gluconeogenesis. This study shows that mTORC2 and dietary potassium coordinate the regulation of sodium-glucose cotransport and glucose production in the kidney via independent mechanisms. New insights into the regulation of these processes in the kidney offer promising implications for diabetes mellitus management and treatment.

physiology↗

bioRxiv2024

MerTK-dependent efferocytosis by monocytic-MDSCs mediates resolution of post-lung transplant injury

ABSTRACTO_ST_ABSRationaleC_ST_ABSPatients with end stage lung diseases require lung transplantation (LTx) that can be impeded by ischemia-reperfusion injury (IRI) leading to subsequent chronic lung allograft dysfunction (CLAD) and inadequate outcomes. ObjectivesWe examined the undefined role of MerTK (receptor Mer tyrosine kinase) on monocytic myeloid-derived suppressor cells (M-MDSCs) in efferocytosis (phagocytosis of apoptotic cells) to facilitate resolution of lung IRI. MethodsSingle-cell RNA sequencing of lung tissue and BAL from post-LTx patients was analyzed. Murine lung hilar ligation and allogeneic orthotopic LTx models of IRI were used with Balb/c (WT), cebpb-/- (MDSC-deficient), Mertk-/- or MerTK-CR (cleavage resistant) mice. Lung function, IRI (inflammatory cytokine and myeloperoxidase expression, immunohistology for neutrophil infiltration), and flow cytometry of lung tissue for efferocytosis of apoptotic neutrophils were assessed in mice. Measurements and Main ResultsA significant downregulation in MerTK-related efferocytosis genes in M-MDSC populations of CLAD patients compared to healthy subjects was observed. In the murine IRI model, significant increase in M-MDSCs, MerTK expression and efferocytosis was observed in WT mice during resolution phase that was absent in cebpb-/- Land Mertk-/- mice. Adoptive transfer of M-MDSCs in cebpb-/- mice significantly attenuated lung dysfunction, and inflammation leading to resolution of IRI. Additionally, in a preclinical murine orthotopic LTx model, increases in M-MDSCs were associated with resolution of lung IRI in the transplant recipients. In vitro studies demonstrated the ability of M-MDSCs to efferocytose apoptotic neutrophils in a MerTK-dependent manner. ConclusionsOur results suggest that MerTK-dependent efferocytosis by M-MDSCs can significantly contribute to the resolution of post-LTx IRI.

immunology↗

bioRxiv2023

TBK1 is ubiquitinated by TRIM5alpha to assemble mitophagy machinery

Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5. Mitochondrial damage triggers TRIM5s auto-ubiquitination and its interaction with ubiquitin-binding autophagy adaptors including NDP52, optineurin, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5 to engage with TBK1. TRIM5 with intact ubiquitination function is required for the proper accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Additionally, we show that TRIM5 can directly recruit autophagy initiation machinery to damaged mitochondria. Our data support a model in which TRIM5 provides a self-amplifying, mitochondria-localized, ubiquitin-based, assembly platform for TBK1 and mitophagy adaptors that is ultimately required to recruit the core autophagy machinery.

cell biology↗

bioRxiv2023

Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant

The mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.

biochemistry↗

bioRxiv2022

Automated neuronal reconstruction with super-multicolour fluorescence imaging

Fluorescence imaging is widely used for the mesoscopic mapping of neuronal connectivity. However, neurite reconstruction is challenging, especially when neurons are densely labelled. Here we report a strategy for the fully automated reconstruction of densely labelled neuronal circuits. Firstly, we established stochastic "super-multicolour" labelling with up to seven different fluorescent proteins using the Tetbow method. With this method, each neuron was labelled with a unique combination of fluorescent proteins, which were then imaged and separated by linear unmixing. We also established an automated neurite reconstruction pipeline based on the quantitative analysis of multiple dyes (QDyeFinder). To classify colour combinations, we used a newly developed unsupervised clustering algorithm, dCrawler, in which data points in multi-dimensional space were clustered based on a given threshold distance. Our new strategy allows for the reconstruction of neurites for up to hundreds of neurons at a millimetre scale without manual tracing.

neuroscience↗

bioRxiv2022

Germline protein, Cup, non-cell autonomously limits migratory cell fate in Drosophila oogenesis.

Attaining migratory fate from a stationary cell population is complex and indispensable both for the multicellular organism development as well for the pathological condition like tumor metastasis. Though widely prevalent in the metazoans, the molecular understanding of this phenomenon remains elusive. Specification of migratory border cells from the follicular epithelium during Drosophila oogenesis has emerged as one of the excellent model systems to study how motile cell are specified. JAK-STAT activation in 6-10 anterior most follicle cells of the Drosophila egg chamber transforms them to a migratory cluster called the border cells. We show that a nurse cell protein, Cup, non-cell autonomously restricts the domain of JAK-STAT activation in the anterior follicle cells. Further examination suggests that Cup functions through Rab11GTPase to regulate Delta trafficking in the nurse cells potentiating Notch activation in the anterior follicle cells. Since Notch activity in the follicle cells modulates the JAK-STAT, any perturbation in Notch activation affects the border cell fate. Altogether, we propose that germline Cup affects the border cell fate through appropriate activation of Notch and JAK-STAT signaling in the follicle cells.

developmental biology↗

bioRxiv2022

Inducible Nitric Oxide Synthase deficiency leads to early demyelination by altering the balance between pro- and anti-inflammatory responses against Murine-β-Coronavirus

The neurological disease Multiple sclerosis (MS) is characterized by neuroinflammation and demyelination orchestrated by the activated glial cells, the CNS infiltrating leukocytes, and their reciprocal interaction through inflammatory signals. Inducible nitric oxide synthase (iNOS), an enzyme that catalyzes sustained nitric oxide production in response to an inflammatory stimulus, is a pro-inflammatory marker expressed particularly by the microglia/macrophages (MG/M{varphi}) during neuroinflammation. In MS, iNOS has been reportedly associated with the disease pathology; however, studies dissecting its role in the underlying mechanisms, specifically demyelination, are limited. Therefore, we studied the role of iNOS in a recombinant beta-coronavirus-MHV-RSA59-induced neuroinflammation, which is a prototypic animal model used to investigate the pathological hallmarks of MS, neuroinflammatory demyelination, and axonal degeneration. During the acute phase of infection with RSA59, wildtype C57BL/6 (WT) mice had significantly upregulated iNOS expression in macrophages, natural killer cells, and natural killer T cells suggesting a role for iNOS in RSA59-induced neuroinflammation. Studies comparing RSA59-infected WT and iNOS-deficient mice revealed that iNOS deficiency aggravated the disease with increased CNS infiltration of macrophages and neutrophils and enhanced mortality. As early as 9-10 days after the infection, the CNS of iNOS-deficient mice had substantially higher demyelination marked with morphologically defined MG/M{varphi} in the demyelinating regions. Transcript analysis confirmed the significant upregulation of type2 macrophage (M2) markers-Arginase 1, CD206, and TREM2-in the CNS of iNOS-deficient mice. Corroborating to the phenotype, the iNOS-deficient mice showed a significantly higher expression of TGF{beta}-an anti-inflammatory cytokine- and increased T regulatory (Treg) cell infiltration, indicating an anti-inflammatory milieu established early after the infection. These observations highlight a protective role of iNOS in virus-induced neuroinflammation whereas its absence leads to MG/M{varphi} polarization towards a phenotype that may be involved in the exacerbated demyelination pathology. Author summaryContrary to the reported pathogenic role of inducible nitric oxide synthase (iNOS) in multiple sclerosis and related autoimmune animal models, we show that the mice deficient in iNOS show an exacerbated disease with accelerated demyelination accompanied by heightened production of an anti-inflammatory and phagocytic markers and more numbers of Tregs in a mouse model of a recombinant mouse hepatitis virus RSA59 infection. Therefore, iNOS may play protective and regulatory roles in this beta-coronavirus infection.

neuroscience↗

bioRxiv2022

Structural features of mTORC2 that control substrate-specific activities.

mTORC2 is a multi-subunit kinase complex that is central to multiple essential signaling pathways. Two core subunits, Rictor and mSin1 distinguish it from its relative, mTORC1 and support context-dependent phosphorylation of its substrates. mTORC2 structures have been determined previously, however, important questions remain, particularly regarding structural determinants of substrate specificity and context dependent activities. We used cryo-EM to obtain high resolution structures of the human mTORC2 apo-complex, as well as structures in the presence of substrates, Akt and SGK1. Specific predictions suggested by substrate-induced structural changes were tested in functional assays. First, side chain interactions between Rictor and mTOR that prevent recruitment of mTORC1 substrates and confer resistance to the mTORC1 inhibitor rapamycin were visualized for the first time in the apo-state, demonstrating the steric occlusion that prevents mTORC2 interaction with mTORC1 substrates and rapamycin. Also in the apo-state, mSin1 was seen to form extensive contacts with Rictor, including a pair of short -helices nestled between two Rictor helical repeat clusters, followed by an extended strand, which makes multiple weak contacts with Rictor helical cluster 1. In co-complex structures, SGK1, but not Akt, markedly altered the conformation of the mSin1 N-terminal extended strand, disrupting multiple weak interactions while inducing a large rotation of mSin1/Arg-83, which comes to interact with a negative patch within Rictor. Mutation of Arg-83 to Ala selectively disrupted mTORC2 dependent phosphorylation of SGK1 but not of Akt, supporting context-dependent substrate selection. These findings provide new structural and functional insights into mTORC2 specificity and context-dependent activities.

biochemistry↗

bioRxiv2021

Toll signaling enhances mosquito antiplasmodial immunity by promoting differentiation of hemocytes to the Megacyte lineage

Silencing Cactus, a suppressor of Toll signaling, in Anopheles gambiae, eliminates Plasmodium ookinetes by enhancing local release of hemocyte-derived microvesicles that promote activation of the mosquito complement-like system. We report that Cactus silencing dramatically increases the proportion of megacytes, a new effector hemocyte subpopulation of large granulocytes, from 5 to 79% of circulating granulocytes. Transcriptomic and morphological analysis, as well as cell counts, in situ hybridization and expression of cell-specific markers, indicate that Cactus silencing triggers granulocyte differentiation into megacytes, a process mediated by the Rel1 transcription factor of the Toll pathway. Megacytes are very plastic cells that can extend long filopodia, tend to form clusters in vivo, and are massively recruited to the basal midgut surface in response to bacterial feeding and Plasmodium infection. We show that hemocyte differentiation to the megacyte lineage greatly enhances mosquito immunity against Plasmodium.

microbiology↗

bioRxiv2021

Interactomic analysis reveals a new homeostatic role for the HIV restriction factor TRIM5α in mitophagy

The protein TRIM5 has multiple roles in anti-retroviral defense, but the mechanisms underlying TRIM5 action are unclear. Here, we used an APEX2-based proteomics approach to identify TRIM5-interacting proteins. Analysis of the TRIM5 interactome found proteins participating in a wide variety of cellular functions including regulating antiviral signaling pathways. We used this data set to uncover a novel role for TRIM5 in mitophagy, an autophagy-based mode of mitochondrial quality control that is compromised in multiple human diseases. Mitochondrial damage triggered the relocalization of TRIM5 to ER-mitochondria contact sites where TRIM5 colocalized with markers of autophagy initiation and autophagosome biogenesis. Furthermore, we found that TRIM5 knockout attenuated both Parkin-dependent and Parkin-independent mitophagy by preventing the recruitment of autophagy regulators FIP200 and ATG13 to unhealthy mitochondria. Finally, TRIM5 knockout cells showed reduced mitochondrial function under basal conditions and were more susceptible to uncontrolled immune activation and cell death in response to mitochondrial damage than were wild type cells. Taken together, our studies have identified a homeostatic role for a protein previously recognized exclusively for its antiviral actions.

cell biology↗

bioRxiv2020

A non-canonical role for the autophagy machinery in anti-retroviral signaling mediated by TRIM5α.

TRIM5 is a key cross-species barrier to retroviral infection, with certain TRIM5 alleles conferring increased risk of HIV-1 infection in humans. TRIM5 is best known as a species-specific restriction factor that directly inhibits the viral life cycle. Additionally, it is also a pattern-recognition receptor (PRR) that activates inflammatory signaling. How TRIM5 carries out its multi-faceted actions in antiviral defense remains incompletely understood. Here, we show that proteins required for autophagy, a cellular self-digestion pathway, play an important role in TRIM5s function as a PRR. Genetic depletion of proteins involved in all stages of the autophagy pathway prevented TRIM5-driven expression of NF-{kappa}B and AP1 responsive genes. One of these genes is the preeminent antiviral cytokine interferon {beta} (IFN-{beta}), whose TRIM5-dependent expression was lost in cells lacking the autophagy proteins ATG7, BECN1, and ULK1. Moreover, we found that the ability of TRIM5 to stimulate IFN-{beta} expression in response to recognition of a TRIM5-restricted HIV-1 capsid mutant (P90A) was abrogated in cells lacking autophagy factors. Stimulation of human macrophage-like cells with the P90A virus protected them against subsequent infection with an otherwise resistant wild type HIV-1 in a manner requiring TRIM5, BECN1, and ULK1. Mechanistically, TRIM5 was attenuated in its ability to activate the kinase TAK1 in autophagy deficient cells, and both BECN1 and ATG7 contributed to the assembly of TRIM5-TAK1 complexes. These data demonstrate a non-canonical role for the autophagy machinery in assembling antiviral signaling complexes and demonstrate a role for autophagy in the establishment of a TRIM5-dependent antiviral state. SIGNIFICANCE STATEMENTTRIM5 is an antiretroviral protein that employs multiple mechanisms to protect cells against infection. Previous studies have linked TRIM5 to autophagy, a cytoplasmic quality control pathway with numerous roles in immunity, raising the possibility that TRIM5 engages autophagy in antiviral defense. This concept has been controversial, since TRIM5s best-known role as a directly acting antiretroviral effector is autophagy independent. However, retroviral restriction is only one aspect of TRIM5 function. We demonstrate that autophagy is crucial to another TRIM5 action: its role as a pattern-recognition receptor. We show that autophagy machinery is required for TRIM5 to transduce antiviral signaling and to establish an antiretroviral state. Our data indicate that autophagy provides TRIM5 with a platform upon which to activate antiviral responses.

cell biology↗

bioRxiv2019

NORTH: a highly accurate and scalable Naive Bayes based ORTHologous gene clustering algorithm

BackgroundThe principal objective of comparative genomics is inferring attributes of an unknown gene by comparing it with well-studied genes. In this regard, identifying orthologous genes plays a pivotal role as the orthologous genes remain less diverged in the course of evolution. However, identifying orthologous genes is often difficult, slow, and idiosyncratic, especially in the presence of multiplicity of domains in proteins, evolutionary dynamics (gene duplication, transfer, loss, introgression etc.), multiple paralogous genes, incomplete genome data, and for distantly related species where similarity is hard to recognize. MotivationAdvances in identifying orthologs have mostly been constrained to developing databases of genes or methods which involve computationally expensive BLAST search or constructing phylogenetic trees to infer orthologous relationships. These methods do not generally scale well and cannot analyze large amount of data from diverse organisms with high accuracy. Moreover, most of these methods involve manual parameter tuning, and hence are neither fully automated nor free from human bias. ResultsWe present NORTH, a novel, automated, highly accurate and scalable machine learning based orhtologous gene clustering method. We have utilized the biological basis and intuition of orthologous genes and made an effort to incorporate appropriate ideas from machine learning (ML) and natural language processing (NLP). We have discovered that the BLAST search based protocols deeply resemble a "text classification" problem. Thus, we employ the robust bag-of-words model accompanied by a Naive Bayes classifier to cluster the orthologous genes. We studied 1,255,877 genes in the largest 250 ortholog clusters from the KEGG database, across 3,880 organisms comprising the six major groups of life, namely, Archaea, Bacteria, Animals, Fungi, Plants and Protists. Despite having more than a million of genes on distantly related species with acute data imbalance, NORTH is able to cluster them with 98.48% Precision, 98.43% Recall and 98.44% F1 score, showing that automatic orthologous gene clustering can be both highly accurate and scalable. NORTH is available as a web interface with a server side application, along with cross-platform native applications (available at https://nibtehaz.github.io/NORTH/) - allowing queries based on individual genes.

bioinformatics↗

bioRxiv2018

Quantitative modelling explains distinct STAT1 and STAT3 activation dynamics in response to both IFNγ and IL-10 stimuli and predicts emergence of reciprocal signalling at the level of single cells

IFN{gamma} and IL10 pathways elicit functionally opposing cell fates, however, these two stimuli activate common transcription factors like STAT1 and STAT3 (S/1/3). How the two stimuli regulate the dynamics of S/1/3 activation remains less understood. Here, we experimentally measured the signaling dynamics of S/1/3 in response to IFN{gamma} and IL10 and found that STAT3, in particular, exhibits a bell-shaped response to both stimuli with maximal activation in an intermediate dose. We built a mathematical model, which quantitatively captured the S/1/3 dynamics and by model analysis, we identified the primary regulators controlling the bell-shaped STAT3 responses in both pathways. As the STATs are activated in response to both stimuli, in a scenario when cells are subjected to co-stimulation of IFN{gamma} and IL10, an interpathway competition to activate the common substrate is plausible. Additionally, a strong transcriptional induction of SOCS1 (a negative regulator of IFN{gamma} pathway) was observed upon IL10 stimulation, suggesting that IL10 pathway can potentially inhibit the IFN{gamma} pathway via SOCS1 induction. To quantitatively understand the S/1/3 responses to co-stimulation we next simulated the same which predicted STAT3 activation and SOCS1 induction dynamics would robustly remain IL10 driven. Subsequent experiments validated the model predictions. Further, the model analysis identified the primary regulators controlling the robustness of IL10-STAT3 axis in co-stimulation. Together, our data-driven model quantitatively captured the dynamics of the STATs in response to both pro (IFN{gamma}) and anti (IL10)-inflammatory stimuli and identifies distinct regulatory elements controlling STAT3 signaling in individual and co-stimulation conditions.

systems biology↗