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Ghosh, J.

Publications and source records attributed to Ghosh, J..

12 recordsLinked to original sources

Modeling Dynamics of Contact Inhibition of Proliferation and Structural Order in a Confluent Epithelium

Contact inhibition of proliferation (CIP) enables epithelial tissues to self-regulate growth and maintain tissue homeostasis. However, how cell-level mechanical contact, tissue-scale structural order, and proliferation kinetics interplay remains a fundamental open question in living matter physics. Here, we present a particle-based model of a confluent epithelial monolayer governed by overdamped dynamics, where individual cells interact via a two-dimensional hard core- soft shoulder potential. By comparing structural evolution during quasistatic densification with previously reported experimental division kinetics, we find that the dynamics of proliferation arrest mimics the onset of direct steric contacts between the hard cores of the shell. Identifying hard core contacts as the physical driver of CIP, we couple our mechanical model with a stochastic Monte Carlo division scheme in which the instantaneous division rate decreases to zero from an intrinsic value as the number of hard core contact increases to six from zero. We demonstrate that for high intrinsic division rates, the cellular densification outpaces mechanical relaxation. This kinetic mismatch drives premature hard-core contact formation, shifts the onset of jamming and contact inhibition to lower packing fractions, and induces increasingly disordered transient configurations before the tissue universally converges to a hexagonal close-packed limit. Our model's predicted division kinetics and structural order evolution are consistent with epithelial monolayer experiments, both reported and our own. This minimal physical framework links single-cell steric contact mechanics directly to tissue-scale growth regulation and structural evolution.

biophysics↗

Leaky scanning translates a conserved ORF in the 3'UTR of RPL36A and regulates the expression of ribosomal protein L36a.

The 3'UTRs of eukaryotic mRNAs are major hubs of post-transcriptional regulation that govern the spatial and temporal regulation of gene expression. Although 3'UTRs were long considered non-coding, recent studies have revealed translation within downstream open reading frames (dORFs) located in 3'UTRs. In contrast to upstream ORFs (uORFs) in 5'UTRs, the mechanisms governing dORF translation and their functional significance remain poorly understood. Here, we identify and characterize a dORF within the 3'UTR of RPL36A, which encodes ribosomal protein L36a. Analysis of ribosome profiling datasets revealed ribosome footprints aligned with the dORF reading frame across multiple human tissues and cell lines. Conservation analysis together with luciferase- and GFP-based reporter assays further supported active translation of the dORF. Using strategically placed RNA hairpin structures and mutational analyses, we show that dORF translation is consistent with ribosomal leaky scanning. Disruption of dORF translation, either by mutating its start codon in exogenous constructs or by CRISPR-mediated deletion of the endogenous dORF-containing region, reduced RPL36A mRNA and protein levels and resulted in impaired global translation. We further identified a miR-5701-binding site within the dORF region and provide evidence that dORF translation antagonizes miR-5701-mediated repression of RPL36A. Finally, we identify a similar dORF-associated regulatory mechanism in RPS3, which encodes ribosomal protein S3. Together, our findings uncover dORF translation as a regulatory mechanism controlling ribosomal protein expression.

molecular biology↗

Sustained presence of metabolically active mesophiles in the boiling vent-water of a low-salinity, slightly-alkaline, sulfate-rich geothermal spring characterized by an inequitable ecology of hyperthermophiles and thermophiles

Geothermal vent-heads exclusively support the proliferation of (hyper)thermophilic microorganisms. However, diverse mesophiles are stochastically thrust into these ecosystems by local geodynamic forces, and their population-level responses to the unfamiliar stressor hold critical implications for lifes intrinsic resilience to biophysical adversities. Here, we report a time-course exploration of the boiling vent-water of a Trans-Himalayan geothermal spring to determine the population dynamics, in situ functionalities, and potential ecological roles of mesophilic incomers in the context of indigenous (hyper)thermophiles. The temporally-consistent (hyper)thermophilic core-community, predominated in turn by a few Aquificia and Thermoproteota, was delineated as metagenome-assembled genomes. Mesophiles/moderate-thermophiles were identified as MAGs and/or pure-cultures, and whether temporally-consistent/inconsistent, had far lower prevalence. Overall, in situ transcriptional activity and prevalence had significant positive correlation; but many species exhibited high activity despite low prevalence and vice versa, implicating the decoupling of global metabolism from growth/proliferation. Bulked metatranscriptomic signatures identified the (hyper)thermophiles as primary producers of the ecosystem. Populations of mesophiles and moderate-thermophiles were apparently active, but not growing, in situ, with some being engaged in environment detoxification, and production of nutrients, metabolites and protective-biomolecules wanting in the (hyper)thermophiles. The findings engender an unprecedented portrayal of geothermal-vents as multi-community ecosystems where unfamiliar immigrants provide critical metabolic services.

microbiology↗

HF-125, a first-in-class computer-modeled novel inhibitor of Tribbles 2, for therapy of enzalutamide resistant, neuroendocrine prostate cancer.

Second generation antiandrogens, such as enzalutamide, are commonly prescribed to treat advanced prostate cancer. However, enzalutamide resistant prostate cancer (ERPC) invariably develops with more aggressive features. Management of ERPC is extremely difficult not only because available therapies cannot effectively eliminate ERPC cells but also due to enhanced growth and highly metastatic features in ERPC cells to invade distant organs. This problem is amplified by the lack of proper knowledge about suitable molecular targets in ERPC cells. Recently, we reported that Tribbles 2 (TRIB2), is overexpressed in ERPC cells and tumors and inhibition of TRIB2 kills ERPC cells via apoptosis. TRIB2 enhances cancer cell growth and invasion and confers resistance to enzalutamide, while inhibition of TRIB2 resensitizes the resistant cells. Interestingly, TRIB2 induces neuroendocrine (NE) features in ERPC cells and both the de novo and treatment-emergent NEPC cells consistently overexpress TRIB2. Though TRIB2 has emerged as a promising target, suitable inhibitors are not commercially available for clinical use. We used artificial intelligence (AI)-based molecular modeling to design a series of small chemical entities with potentially high specificity to bind with TRIB2. Extensive virtual screening and molecular editing yielded few highly selective and potent agents to inhibit TRIB2 and kill ERPC-NE/NEPC cells. One such compound (HF-125) directly binds to destabilize and degrade TRIB2 proteins involving proteasomes and is effective both in vitro and in vivo. Based on these findings, HF-125 emerges as a promising novel agent for development of a new therapeutic strategy for ERPC-NE/NEPC types of aggressive prostate cancer.

cancer biology↗

Psychrophilic and cryophilic bacterial copiotrophs from a Trans-Himalayan lake-desert ecosystem as biogeothermometers of warming, mitigators of perturbation, and candidates for biodegradation

A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of native copiotrophic psychrophiles that have the potentials for rendering substantive carbon remineralization under natural and/or anthropogenically influenced conditions of high organic matter delivery to the environment. Overall 27 species, classified across 15 genera of Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota, were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lacustrine body on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth, all the isolates grew at 4{degrees}C and 15{degrees}C; 13 of them grew, while 14 retained 19-99% cells in metabolically-active state, at -10{degrees}C; 23, 11, and none grew at 28{degrees}C, 37{degrees}C, and 42{degrees}C respectively. A Cryobacterium was most heat-susceptible, whereas some -10{degrees}C-growing Arthrobacter, Microbacterium, Paenarthrobacter, Pseudomonas and Streptomyces were most warming-resilient, among the present isolates. Catabolizing different simple/complex organic compounds, all isolates accomplished low/moderate/high growths at 4{degrees}C; 20 performed low growths at -10{degrees}C. Taxonomy/phylogeny did not determine the isolates growth/survival across the temperature-range tested. Lake-water and rock-dust isolates had the widest, while lake-sediment-dwellers had the narrowest, temperature-window for growth/survival. Rock-dust and lake-water isolates had more genes for low and high temperature adaptations, compared to the lake-sediment isolates. In co-cultures, most actinobacterial isolates inhibited the growth of mesophilic bacteria from warmer ecosystems, plus non-actinobacteria and actinobacteria from native/adjoining habitats. The data hold implications for biodegradation in cold/frigid territories, negative feedback control/reversal of warming, and microbiome protection from infiltration amidst climate change. IMPORTANCEPhylogenetically diverse, cold-adapted copiotrophic bacteria were retrieved from a Trans-Himalayan lake-desert ecosystem, and tested for chemoorganoheterotrophic growth at temperatures between -10{degrees}C and 42{degrees}C. Albeit growth dwindled at [≥]28{degrees}C, most of the isolates thrived on simple as well as complex organic substances under freezing condition, which makes them prospective constituents of biodegradation reactors suitable for high-altitude/latitude deployment. In the natural habitats of the psychrophilic isolates, cessation of organotrophic activities at elevated temperatures would stop simple fatty acids and CO2 production, which in turn would preempt methanogenesis, undo greenhouse effect, and reverse environmental thawing (usher cooling). Such negative feedback control of homeostasis is fraught with the danger of microbiome takeover by thermally-better-adapted foreign organisms. Consequently, ecosystem preservation rests on the native microfloras ability to resist external invasion. At 28{degrees}C, majority of the actinobacterial isolates inhibited bacteria from discrete higher-temperature ecosystems; they can, therefore, be viewed as the defenders of the cold/frigid ecosystem.

microbiology↗

Lead optimization against drug-resistant Leishmania donovani infection: Semi-synthetic derivatives of ethyl linoleate isolated from Indian edible mushroom Meripilus giganteus.

Visceral leishmaniasis, the most severe form, affects thousands of people annually. Current drugs in practice fail to provide an absolute cure. Globally, treatment relies on a single dose of liposomal amphotericin B, which requires a costly setup and cold chain to maintain. Natural molecules remain the vital sources of therapeutic ingredients in modern medicine. Meripilus giganteus is traditionally consumed by the people of the North-eastern regions of the Himalayas, India. In this study, we planned for the stepwise bioactivity-guided isolation of natural molecules from M. giganteus and to synthesize more potential therapeutic derivatives against the drug-resistant Leishmania infection. HPLC chromatogram of ethyl acetate extract obtained from M. giganteus revealed the presence of ethyl linoleate as the most active anti-leishmanial molecule. Several derivatives of ethyl linoleate were synthesized and evaluated against Leishmania promastigotes. Among them, a single epoxygenated variant of ethyl linoleate, ethyl (Z)-8-(3-(oct-2-en-1-yl) oxiran-2-yl) octanoate (EL3), showed promising anti-leishmanial activity against both drug-sensitive and drug-resistant Leishmania donovani. The lead derivative disrupts the biosynthesis of trypanothione from glutathione and spermidine, making the parasite vulnerable to the oxidative burst inside the host. Interestingly, the lead derivative was found to be more efficient against the drug-resistant L. donovani, in vivo. Besides this, it has almost no toxicity towards host cells. Considering the urgency for new drug development, we propose this novel semi-synthetic derivative as a potent therapeutic lead.

immunology↗

A detailed study Biofilm forming Polyextremophilic Firmicutes from the Himalayas and exploration of their plant growth promoting potential.

Polyextremophily has been an intriguing point of interest among the scientists, a phenomenon in which organisms can thrive in combinations of multiple extreme conditions. In the foreseeable future, climatic conditions are predicted to change, and agriculture is bound to suffer with these changes in the environment. The situation necessitates some solutions that can ensure agricultural sustainability, in the changed, harsh environmental conditions without more toxic chemical intrusions in the agricultural fields. The bacterial strains Brevibacillus parabrevis BRAM_Y3 and Mesobacillus subterraneous BRAM_Y2 in this study, isolated from the waters of Yamunotri showed incredible properties of Polyextremophily like tolerance to not only temperatures as high as 70{degrees}C, pH range (4-10), saline, drought, UV and heavy metals such as mercury, iron, silver and arsenic but also their two-dimensional and three-dimensional combinations. The elevated levels of biofilm formation when subjected to stress revealed their property of using biofilm as their shield against harsh conditions. Furthermore, they were studied for their plant growth promotion like nutrient sequestration (N, P, K, plant hormone production etc.) biocontrol properties (cell wall degrading enzymes, siderophores, VOCs etc.) and the ability to confer abiotic stress resistance (ACC Deaminase) to plants. The in-vivo experiments conducted on Zea mays. L yielded conclusive and promising results. The use of these polyextremophiles for agriculture in harsh environments may serve as a solution for the global warming mediated climate and environmental changes.

microbiology↗

Decoding Host-Pathogen Interactions in Staphylococcus aureus: Insights into Allelic Variation and Antimicrobial Resistance Prediction Using Artificial Intelligence and Machine Learning based approaches

This novel study leveraged advanced machine learning techniques to elucidate the molecular mechanisms of antimicrobial resistance (AMR) in 300Staphylococcus aureus isolates across six critical antibiotics. Employing a diverse array of deep learning and ensemble models, we conducted an in-depth analysis of genetic markers and allelic variations to characterize resistance determinants. Our investigation revealed that the XGBoost ensemble model demonstrated the most exceptional performance, achieving a remarkable 95% test accuracy, 100% training accuracy, and an unprecedented ROC AUC of 0.9855. Comparative analysis of multiple machine learning approaches, including Long Short-Term Memory (LSTM), Convolutional Neural Network (CNN), Multi-Layer Perceptron (MLP), Decision Tree, and Stochastic Gradient Descent (SGD) models, provided detailed insights into resistance prediction. The SHAP (SHapley Additive exPlanations) analysis unveiled critical genetic markers, with "cat_allele_Cluster_1015_Allele_8" emerging as the most influential feature driving resistance predictions. Notably, the models exhibited varying performance across different antibiotics, with consistently high accuracy and F1-scores for ciprofloxacin, clindamycin, gentamicin, and sulfamethoxazole/trimethoprim. Our findings not only demonstrate the potential of advanced machine learning techniques in predicting antimicrobial resistance but also provide crucial insights into the molecular mechanisms underlying S. aureus drug resistance. By identifying key genetic determinants and their relative importance, this study offers a sophisticated approach to understanding resistance patterns, potentially guiding future diagnostic strategies, targeted therapies, and antimicrobial stewardship practices in clinical settings.

bioinformatics↗

DNA polymerase theta-mediated DNA repair is a functional dependency and therapeutic vulnerability in DNMT3A deficient leukemia cells

Myeloid malignancies carrying somatic DNMT3A mutations (DNMT3Amut) may be refractory to standard therapy. DNMT3Amut leukemia cells accumulate toxic DNA double strand breaks (DSBs) and stalled replication forks, rendering them dependent on DNA damage response (DDR). We report here that DNA polymerase theta (Pol{theta}), a key element in DSB repair by end-joining (TMEJ) and in fork restarting, is essential for survival and proliferation of DNMT3Amut leukemia cells. Pol{theta} is overexpressed in DNMT3Amut leukemia cells due to abrogation of PARP1 PARylation-dependent UBE2O E3 ligase-mediated ubiquitination and proteasomal degradation of Pol{theta}. In addition, PARP1-mediated recruitment of the SMARCAD1-MSH2/MSH3 repressive complex to DSBs was diminished in DNMT3Amut leukemia cells which facilitated loading of Pol{theta} on DNA damage and promoting TMEJ and replication fork restart. Pol{theta} inhibitors enhanced the anti-leukemic effects of standard drugs such as FLT3 kinase inhibitor quizartinib, cytarabine +/- doxorubicin, and etoposide in vitro and in mice with DNMT3Amut leukemia. Altogether, Pol{theta} is an attractive target in DNMT3Amut hematological malignancies.

cancer biology↗

Identification of New In Vivo TonB-FepA Rendezvous Sites

The TonB system of Gram-negative bacteria uses the protonmotive force of the cytoplasmic membrane to energize active transport of large or scarce nutrients across the outer membrane by means of customized beta-barrels known as TonB-dependent transporters (TBDTs). The lumen of each TBDT is occluded by an amino-terminal domain, called the cork, which must be displaced for transport of nutrients or translocation of the large protein toxins that parasitize the system. A complex of cytoplasmic membrane proteins consisting of TonB, ExbB and ExbD harnesses the protonmotive force that TonB transmits to the TBDT. The specifics of this energy transformation are a source of continuing interest. The amino terminal domain of a TBDT contains a region called the TonB box, that is essential for the reception of energy from TonB. This domain is the only identified site of in vivo interaction between the TBDT and TonB, occurring through a non-essential region centered on TonB residue Q160. Because TonB binds to TBDTs whether or not it is active or even intact, the mechanism and extent of cork movement in vivo has been challenging to discover. In this study, we used in vivo disulfide crosslinking between eight engineered Cys residues in Escherichia coli TonB and 42 Cys substitutions in the TBDT FepA, including the TonB box, to identify novel sites of interaction in vivo. The TonB Cys substitutions in the core of an essential carboxy terminal amphipathic helix (residues 199-216) were compared to TonB Q160C interactions. Functionality of the in vivo interactions was established when the presence of the inactive TonB H20A mutation inhibited them. A previously unknown functional interaction between the hydrophilic face of the amphipathic helix and the FepA TonB box was identified. Interaction of Q160C with the FepA TonB box appeared to be less functionally important. The two different parts of TonB also differed in their interactions with the FepA cork and barrel turns. While the TonB amphipathic helix Cys residues interacted only with Cys residues on the periplasmic face of the FepA cork, TonB Q160C interacted with buried Cys substitutions within the FepA cork, the first such interactions seen with any TBDT. Both sets of interactions required active TonB. Taken together, these data suggest a model where the amphipathic helix binds to the TonB box, causing the mechanically weak domain of the FepA cork to dip sufficiently into the periplasmic space for interaction with the TonB Q160 region, which is an interaction that does not occur if the TonB box is deleted. The TonB amphipathic helix also interacted with periplasmic turns between FepA {beta}-strands in vivo supporting a surveillance mechanism where TonB searched for TBDTs on the periplasmic face of the outer membrane.

molecular biology↗

Tribbles 2 confers enzalutamide resistance in prostate cancer by promoting lineage plasticity.

Second-generation anti-androgen, such as enzalutamide (Xtandi), is commonly prescribed for prostate cancer therapy, but enzalutamide-resistant, lethally incurable disease invariably develops. To understand the molecular basis of enzalutamide resistance, we comprehensively analyzed prostate tumors and clinically relevant models. These studies revealed that enzalutamide resistant prostate cancer cells overexpress Tribbles 2 (Trib2), a pseudokinase. Expression of Trib2 is negatively regulated by androgen receptor signaling. Overexpression of Trib2 makes prostate cancer cells completely resistant to clinically relevant doses of enzalutamide. Trib2 downregulates expression of luminal markers but upregulates the neuronal transcription factor, BRN2, and the stemness factor, SOX2, to induce neuroendocrine differentiation. Our findings indicate that Trib2 confers resistance to enzalutamide therapy via a mechanism involving increased cellular plasticity and lineage switching.

cancer biology↗

Osteogenic differentiation potential and marker gene expression of different porcine bone marrow mesenchymal stem cell subpopulations selected in different basal media

Multipotent porcine mesenchymal stem cells (pMSC) are indispensable for research and therapeutic use. Derivation and culture media might affect the selection of MSC subpopulation and thus the differentiation potential of cells. In this study we evaluated the effects of MEM, aDMEM, M199, MEM/M199, aDMEM/M199 and MEM/aDMEM media on porcine bone marrow MSC derivation; pre-differentiation expression of ALP, COL1A1, SPP1 and BGLAP osteogenic marker genes at passage 5 and 10 pMSC; and differentiation potential of passage 5 pMSC. Morphological changes and matrix formation in osteogenic cells were evaluated by microscopical examination and calcium deposit in osteocytes was confirmed by Alizarin Red S staining. Results indicated media independent selection of different bone marrow MSC subpopulations with different surface marker gene expressions. Many pMSC subpopulations in different media had CD14+ expressing cells. We also observed basal media dependent changes in osteogenic markers expression and differentiation potential of pMSC. The MEM/aDMEM media grown pMSC showed best osteogenic differentiation potential. We thus recommended the testing of MEM/aDMEM mixed media in other species for pre-differentiation MSC culture that are intended for better osteogenic differentiation. SummaryPre-differentiation basal media influence osteogenic differentiation potential of mesenchymal stem cells (MSC). Among the tested media, MEM/aDMEM was the best for pre-differentiation porcine MSC culture intending to use in osteogenesis.

molecular biology↗