Biology subjects

Ghose, D.

Publications and source records attributed to Ghose, D..

12 recordsLinked to original sources

bioRxiv2026

Programming Targeted Immune Cell Migration Using Orthogonal Chemokine-Receptor Pairs

Chemokines orchestrate the migration of immune cells throughout the body, but harnessing chemokine signaling to engineer targeted cell trafficking is challenging because of their overlapping interactions and broad expression patterns. Here we used structure-guided protein design to engineer orthogonal chemokine-receptor pairs with minimal crosstalk to native systems. T cells engineered with an ortho-receptor selectively infiltrated tissues producing the ortho-chemokine, in vitro and in vivo. By engineering T cells that both sense and secrete the ortho-chemokine, we generated collective swarming behavior in which pioneer cells attract follower cells via an ortho-chemokine gradient self-organized by positive feedback. By providing orthogonal genetic control over both the generation and sensing of chemokine gradients, this system enables the construction of autonomous spatial targeting programs in engineered cells.

synthetic biology↗

bioRxiv2026

Human fallopian tube-on-a-chip for preclinical testing of non-hormonal contraceptives with living human sperm

The fallopian tube serves as a sperm reservoir, and it is the site where the oocytes become fertilized. Here, we describe development of an organ-on-a-chip microfluidic model of the fallopian tube (FT Chip) lined by primary human epithelial cells and stromal fibroblasts derived from the FT ampulla. Abundant tissue folds lined by hormone-responsive, epithelial cells resembling those seen in vivo formed on-chip, but not in epithelial organoids cultured in gel cultures. Comparative time-resolved analysis of human sperm versus oocyte-sized microparticles introduced into the epithelial channel in the presence of estradiol revealed that sperm movement was significantly reduced, while the oocyte-sized particles increased, relative to movements in acellular chips. When the non-hormonal contraceptive TDI-11861 was administered to the chip, dose-dependent inhibition of human sperm motility was detected. Thus, this FT Chip may offer a human preclinical tool to study FT physiology and assess the efficacy and mechanism of action of contraceptives.

cell biology↗

bioRxiv2025

Cytokines control the physical state of immune tissue

Unlike most solid-like tissues, immune tissue is protean and reconfigurable--its component cells can patrol vast territories, find rare cellular partners, and dynamically self-organize into functional structures like germinal centers or tertiary lymphoid structures. The ability of immune cells to collectively behave as an active material that switches physical state is essential for adaptive immunity. Yet the principles governing the control of the physical properties of immune tissues, and how chemical and mechanical forms of control interplay remain obscure. Inspired by minimal immune cell components that recapitulate germinal center (GC) dynamics, we developed an agent-based model that predicted that a tissues ability to program its own physical properties governs the efficiency of antibody evolution. This motivated our search for biomolecular forms of control capable of tuning this material property. Using a tractable in vitro model, we found that CD40L-stimulated human B cells self-organize into active, liquid-like condensates that round, fuse, and internally mix. GC cytokines IL-4 and IL-21 tuned this effective temperature, driving phase transitions from cohesive, liquid-like states to dispersed, gas-like morphologies. These findings demonstrate that cytokines control tissue fluidity, suggesting a previously unrecognized biophysical form of immune regulation. Significance StatementThe bodys immune system is uniquely flexible, allowing cells to organize into temporary structures, like germinal centers or tertiary lymphoid structures, to fight intruders. How this physical flexibility is controlled is a major question. We discovered that the physical state of immune tissue is chemically programmable. We show that self-organized multicellular B cell structures behave like liquid droplets, and we used this framework to demonstrate that signals (cytokines) can modulate their physical properties. This finding identifies a new biophysical axis of immune control, suggesting the body actively tunes its tissue fluidity to optimize the immune response.

biophysics↗

bioRxiv2025

Local collective memory from ratiometric signaling outperforms cellular gradient sensing limits

Cells excel at interpreting noisy chemical gradients to guide fertilization, development, and immune responses, but the mechanisms underlying this remarkable ability remain poorly understood. Previous work showed that some G protein signaling pathways can overcome challenges from uneven receptor distribution by using a ratiometric signaling strategy. In this mechanism, G proteins receive information from both bound and unbound receptors, unlike classical signaling where only bound receptors contribute. Here, we show that ratiometric signaling also provides an unexpected ability to suppress noise from low receptor numbers. The benefit stems from each G protein remembering the last receptor state it encountered, so that at any instant, ratiometric G protein collectives reflect time-averaged receptor activity. Unlike classical signaling, this averaging remains unbiased and accurate across the varying ligand concentrations present in a spatial gradient. Using theory and simulations, we demonstrate that this averaging mechanism allows cells to surpass theoretical limits for gradient detection from instantaneous receptor information alone. Our findings reveal how ratiometric biochemical architectures enable robust temporal integration across spatially varying signals, providing cells with enhanced directional accuracy under noisy conditions.

biophysics↗

bioRxiv2023

Rho and a riboswitch regulate mntP expression evading manganese stress and membrane toxicity

The trace metal ion manganese in excess is toxic. Therefore, a small subset of factors tightly maintains its cellular level, among which an efflux protein MntP is the champion. Multiple transcriptional regulators and a manganese-dependent translational riboswitch regulate the MntP expression. As riboswitches are untranslated RNAs, they are often associated with the Rho-dependent transcription termination in bacteria. Here we demonstrate that Rho efficiently terminates transcription at the mntP riboswitch region. The addition of manganese activates the riboswitch, thereby restoring the coupling between transcription and translation to evade Rho-dependent transcription termination partially. Deletion of the riboswitch abolishes Rho-dependent termination and renders bacteria sensitive to manganese due to overexpression of mntP. The high mntP expression is associated with reactive oxygen species (ROS) production, slow growth, and cell filamentation phenotypes. We posit that manganese-dependent transcriptional activation in the absence of Rho-dependent termination leads to the observed toxicity arising from excessive MntP expression, a membrane protein. Thus, we identified a novel regulatory role of Rho in preventing membrane protein toxicity by terminating at the riboswitch element.

biochemistry↗

bioRxiv2022

Prioritizing landscapes to reconcile biodiversity conservation, ecosystem services, and human well-being in India

Biodiversity conservation and human well-being are tightly interlinked; yet mismatches in the scale at which both priorities are planned and implemented have exacerbated biodiversity loss, erosion of ecosystem services, and declining human quality of life. India houses the second largest human population on the planet, while <5% of the countrys land area is effectively protected for conservation. This warrants landscape-level conservation planning through a judicious mix of land-sharing and land-sparing approaches, and co-production of ecosystem services. Through a multi-faceted assessment, we prioritize spatial extents of land parcels that, in the face of anthropogenic threats, can safeguard conservation landscapes across Indias biogeographic zones. We find that only a fraction (~15%) of such priority areas identified here are encompassed under Indias extant PA network, and several landscapes of high importance were omitted in all previous global-scale assessments. We then examined the spatial congruence of priority areas with administrative units earmarked for economic development by the Indian government, and propose management-zoning through state-driven and participatory approaches. Our spatially explicit insights can help meet the twin goals of biodiversity conservation and sustainable development in India and other countries across the Global South.

ecology↗

bioRxiv2022

Discovery of diverse human BH3-only and non-native peptide binders of pro-apoptotic BAK indicate that activators and inhibitors use asimilar binding mode and are not distinguished by binding affinity or kinetics

Apoptosis is a programmed form of cell death important for the development and maintenance of tissue homeostasis. The BCL-2 protein family controls key steps in apoptosis, dysregulation of which can lead to a wide range of human diseases. BCL-2 proteins comprise three groups: anti-apoptotic proteins, pro-apoptotic proteins, and BH3-only proteins. BAK is one of two pro-apoptotic proteins, and previous work has shown that binding of certain BH3-only proteins such as truncated BID (tBID), BIM, or PUMA to BAK leads to mitochondrial outer membrane permeabilization, the release of cytochrome c, and ultimately cell death. This process, referred to as activation, involves the BH3-stimulated conversion of BAK from monomer to dimer and then to oligomers that promote membrane disruption. Crystal structures of putative intermediates in this pathway, crosslinking data, and in vitro functional tests have provided insights into the activation event, yet the sequence-function relationships that make some but not all BH3-only proteins function as activators remain largely unexamined. In this work, we used computational protein design, yeast surface-display screening of candidate BH3-like peptides, and structure-based energy scoring to identify ten new binders of BAK that span a large sequence space. Among the new binders are two peptides from human proteins BNIP5 and PXT1 that promote BAK activation in liposome assays and induce cytochrome-c release from mitochondria, expanding current views of how BAK-mediated cell death may be triggered in cells. High-resolution crystal structures and binding experiments revealed a high degree of similarity in binding geometry, affinity, and association kinetics between peptide activators and inhibitors, including peptides described previously and those identified in this work. We propose a model for BAK activation that is based on differential engagement of BAK monomers vs. the BAK activation transition state that integrates our observations with previous reports of BAK binders, activators, and inhibitors.

biochemistry↗

bioRxiv2021

Free spermidine evokes superoxide radicals that manifest toxicity

Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic to Escherichia coli unless it is neutralized by SpeG, an enzyme for the spermidine N-acetyl transferase function. Besides, a specific mechanism of SpeG function conferring pathogenic fitness to Staphylococcus aureus USA300 strain is unknown. Here, we provide evidence that although spermidine mitigates oxidative stress by lowering hydroxyl radical and hydrogen peroxide levels, excess of it simultaneously triggers the production of superoxide radicals, thereby causing toxicity in the E. coli {Delta}speG strain as well as naturally SpeG-deficient S. aureus RN4220 strain. However, wild-type E. coli and S. aureus USA300 with a horizontally-acquired speG gene tolerate applied exogenous spermidine stress. Furthermore, we demonstrate that while RNA-bound spermidine inhibits iron oxidation, free spermidine interacts and oxidizes the iron to evoke superoxide radicals directly. Superoxide radicals thus generated, further affects redox balance and iron homeostasis. Since iron acquisition and metabolism in the host tissues is a challenging task for S. aureus, the current findings helped us explain that the evolutionary gain of SpeG function by S. aureus USA300 strain allows it to neutralize exogenous spermidine- and spermine-mediated toxicity towards iron metabolism inside the host tissues.

biochemistry↗

bioRxiv2021

Kenyan Traditional Medicine: Exploring Old Solutions to the Modern Antibacterial Crises Through Natural Products Chemistry

Infectious diseases are a major cause of morbidity and mortality around the world, accounting for approximately 50% of all deaths in tropical countries. Despite remarkable progress in the field of microbiology, inability to control or mitigate, epidemics caused by drug-resistant microorganisms pose a serious health hazard to the global population. New therapeutic strategies must be developed as a global initiative for the prevention and control of infectious diseases. This study focuses on Kenyan medicinal plants and their activity against bacteria. Plant extracts obtained from seven Kenyan plants used in traditional medicine, were screened for their antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus, and Mycobacterium smegmatis. Extracts from all these plants showed antibacterial activity against at least one of the tested organisms at a concentration of 2 mg/mL. Chemical screening showed the presence of different classes of phytochemicals such as alkaloids, terpenes, tannins, in some active extracts.

microbiology↗

bioRxiv2020

Swi6/HP1 binding to RNA-DNA hybrids initiates heterochromatin assembly at the centromeric dg-dh repeats in Fission Yeast

Canonically, heterochromatin formation in fission yeast and metazoans is initiated by di/trimethylation of histone H3 at lysine 9 position by the histone methyltransferase Suv39H1/Clr4, followed by binding of Swi6/HP1 to H3-K9-me2/me3 via its chromodomain. Subsequent self-association of Swi6/HP1 on adjacent nucleosomes or a cooperative interaction between Clr4 and Swi6/HP1 leads to folded heterochromatin structure. HP1 binding to RNA is shown to facilitate its localization at and assembly of heterochromatin in metazoans. Likewise, recruitment of Swi6/HP1 to centromere depends on the RNAi pathway in fission yeast; paradoxically, Swi6/HP1 is also thought to play a role in RNA turnover. Here we provide evidence in support of RNAi-independent recruitment of Swi6. We show that, apart from the low affinity binding to RNAs through its hinge domain, as already reported, Swi6/HP1 displays a hierarchy of increasing binding affinity through its chromodomain to the siRNAs corresponding to specific dg-dh repeats and even stronger binding to the cognate siRNA-DNA hybrids than to the siRNA precursors or general RNAs. Our results support a mechanism of recruitment of Swi6, which is dependent on its specific and high affinity binding to siRNA-DNA hybrid at the dg-dh repeats. This binding, which is independent of, albeit augmented by binding to H3-K9-Me2, leads to heterochromatin formation and silencing. We suggest that the net role of Swi6 in RNA physiology may be regulated by a balance between abundance and affinity of Swi6 towards heterochromatic and euchromatic RNAs and siRNAs.

genetics↗

bioRxiv2020

Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae

Yeast decode pheromone gradients to locate mating partners, providing a model for chemotropism. How yeast polarize toward a single partner in crowded environments is unclear. Initially, cells often polarize in unproductive directions, but then they relocate the polarity site until two partners polarity sites align, whereupon the cells "commit" to each other by stabilizing polarity to promote fusion. Here we address the role of the early mobile polarity sites. We found that commitment by either partner failed if just one partner was defective in generating, orienting, or stabilizing its mobile polarity sites. Mobile polarity sites were enriched for pheromone receptors and G proteins, and we suggest that such sites engage in an exploratory search of the local pheromone landscape, stabilizing only when they detect elevated pheromone levels. Mobile polarity sites were also enriched for pheromone secretion factors, and simulations suggest that only focal secretion at polarity sites would produce high pheromone concentrations at the partners polarity site, triggering commitment.

cell biology↗

bioRxiv2018

Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation

The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as Pol I simultaneously polymerizes and depolymerizes at the nick sites utilizing energy-rich dNTPs. Using an in vitro assay system, we demonstrate that the {beta}-clamp of the Escherichia coli replisome strongly inhibits nick translation on the DNA substrate. To do so, {beta}-clamp inhibits the strand displacement activity of Pol I by interfering with the interaction between the finger subdomain of Pol I and the downstream primer-template junction. Conversely, {beta}-clamp stimulates the 5 exonuclease property of Pol I to cleave single nucleotides or shorter oligonucleotide flaps. This single nucleotide flap removal at high frequency increases the probability of ligation between the upstream and downstream DNA strands at an early phase, terminating nick translation. Besides {beta}-clamp-mediated ligation helps DNA ligase to seal the nick promptly during the maturation of Okazaki fragments.

biochemistry↗