Biology subjects

De, D.

Publications and source records attributed to De, D..

9 recordsLinked to original sources

bioRxiv2025

Indirect Deuterium Displacement Exchange Imaging for Non-invasive High-Resolution CSF Production Mapping

Cerebrospinal fluid (CSF) production is central to brain homeostasis, yet existing measurement techniques are invasive, technically demanding, and confounded by intracranial perturbations. Here, we introduce indirect deuterium displacement exchange imaging (CSF-iDDxI), a noninvasive MRI approach for mapping CSF production in vivo. The method leverages intravenously infused deuterium oxide (D2O), which crosses the blood-CSF barrier, replaces existing H2O in CSF, producing concentration-dependent attenuation of proton (1H) signal within CSF spaces. Using high-resolution 3D balanced steady-state free precession MRI in rats, we demonstrate robust and spatially widespread D2O-induced CSF signal loss that is selectively suppressed by acetazolamide, a carbonic anhydrase inhibitor known to suppress CSF production by the choroid plexus. Dynamic imaging during intravenous D2O infusion further revealed that cortical parenchymal signal changes were unaffected by acetazolamide, confirming specificity to CSF production. Exploratory kinetic modeling estimated rapid CSF water turnover (k {approx} 0.09 min-1) under physiological conditions, reduced to k {approx} 0.031 min-1 with acetazolamide suppression, consistent with prior isotope tracer studies. Together, these findings establish CSF-iDDxI as a sensitive, pharmacologically validated tool for quantifying CSF production and turnover.

neuroscience↗

bioRxiv2025

Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients

Colorectal cancer (CRC) diagnosed before age 50 years (early-onset CRC, EO-CRC) is rising at an alarming rate, yet its molecular and microenvironmental drivers remain poorly understood. EO-CRC is highly heterogeneous, and while subtle differences from late-onset CRC (LO-CRC) have been reported, their full extent remains unresolved due to the limited scope of previous studies. Here, we integrate public data with in-house clinical samples profiled by single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence (mIF) to compare EO-CRC and LO-CRC. Additionally, we employ gene regulatory network-based protein activity inference (VIPER), enabling a more precise characterization of key regulatory proteins driving tumor-stroma interactions. Our analysis reveals that EO-CRC and LO-CRC have a largely similar immune composition, challenging previous reports of an "immune-cold" phenotype in EO-CRC. However, we identify distinct stromal differences, including a significant enrichment of fibroblasts in EO-CRC. Notably, we define a previously unrecognized epithelial subpopulation in EO-CRC, marked by high expression of toll-like receptor 4 (TLR4) and C-C chemokine receptor type 5 (CCR5)--key mediators of inflammation-driven tumor progression and fibroblast recruitment. These findings suggest that EO-CRC may be driven by a tumor-intrinsic inflammatory phenotype with enhanced stromagenesis, providing new insights into potential mechanisms underlying its increasing incidence in young adults.

cancer biology↗

bioRxiv2024

Supplemental Dietary Nano Zinc Can Impart Higher Antioxidant Status by Modulating Cu-Zn SOD Expression

Zinc seems to be the most critical micronutrients dietary adequacy of which ensures optimum health and body defence. Considering its immunomodulation potency, zinc is often used for dietary fortification more particularly in face of challenges. However indiscriminate use of zinc as therapeutic agent often leads to secondary deficiencies of other critical nutrients due to the unwanted antagonism with other interacting nutrients available in gut. In the present study we targeted to devise a nano-structured zinc which will remain inert to other dietary micronutrients present in gut to ensure its high bioavailability. An environment benign colloidal chemistry route was employed for the synthesis of nano-dimensional zinc oxide. The microanalytical characterizations revealed that the apparent particle size of our nano-Zinc oxide ranged between 30-40 nm. The as-synthesized ZnO-NP was used for dietary fortification and the MTT assay confirmed the safe limit for its dietary inclusion. The antioxidant potential of the synthesized nano-zinc was evaluated in milk fish (Chanos chanos) considering it as a model organism. We have employed Cu-Zn SOD gene as molecular marker for antioxidant assessment with integral zinc binding sites. We have characterized Cu-Zn SOD gene in Chanos chanos for the first time and identified certain important zinc binding sites present in the Cu-Zn SOD. A significantly better expression profile of Cu-Zn SOD was observed among the fish fed dietary ZnO-NP and the best effect was observed when the fish feed was fortified with 20 ppm ZnO-NP. The outcome of this study ensures the higher bioavailability of the synthesized ZnO-NP to be assimilated into Cu-Zn SOD, which in turn imparts higher body antioxidant. Nano zinc being inert, may directly bind through the zinc binding sites of Cu-Zn SOD molecules thereby leads to its better expression and more antioxidant status through molecular interaction with other molecules through longevity regulating pathway as explored by the String and KEGG pathway analysis carried out in the present investigation.

genomics↗

bioRxiv2024

Screening of glucose binding proteins for the development of biosensors

Selecting suitable glucose-binding proteins (GBPs) is vital for biosensor development for medical diagnostics and quality control in the food industry. Biosensors offer advantages such as high specificity, selectivity, fast response time, continuous measurement, and cost-effectiveness. The current work utilized a combination of molecular docking, molecular dynamics (MD) simulations, and free energy calculations to develop a high-throughput bioinformatics pipeline to select GBP candidates from an extensive protein database (37,325 proteins). Using molecular docking, GBPs with good binding affinity to glucose (1,447 candidates) were virtually screened from the Protein Data Bank. MD simulations ascertained the binding dynamics of a few selected candidates. Further, steered MD (Brownian dynamics fluctuation-dissipation-theorem) was used to estimate binding free energies of the ligand-protein complex. Correlations between ligand-binding parameters obtained from longer MD simulations and binding parameters interpreted from significantly faster docking simulations were investigated. The correlation plots suggested that a combination of threshold values of the following three docking parameters: docking binding energy, binding cavity depth, and the number of hydrogen bonds between the ligand and binding site residues can be used to predict candidate GBPs reliably. Thus, a high-throughput and accurate protein selection process based on relatively faster docking simulations was proposed to screen GBPs for glucose biosensing.

bioinformatics↗

bioRxiv2023

Arrest of mouse preterm labor until term delivery by combination therapy with atosiban and mundulone, a natural product with tocolytic efficacy

Currently, there is a lack of FDA-approved tocolytics for the management of preterm labor (PL). In prior drug discovery efforts, we identified mundulone and its analog mundulone acetate (MA) as inhibitors of in vitro intracellular Ca2+-regulated myometrial contractility. In this study, we probed the tocolytic and therapeutic potential of these small molecules using myometrial cells and tissues obtained from patients receiving cesarean deliveries, as well as a mouse model of PL resulting in preterm birth. In a phenotypic assay, mundulone displayed greater efficacy in the inhibition of intracellular-Ca2+ from myometrial cells; however, MA showed greater potency and uterine-selectivity, based IC50 and Emax values between myometrial cells compared to aorta vascular smooth muscle cells, a major maternal off-target site of current tocolytics. Cell viability assays revealed that MA was significantly less cytotoxic. Organ bath and vessel myography studies showed that only mundulone exerted concentration-dependent inhibition of ex vivo myometrial contractions and that neither mundulone or MA affected vasoreactivity of ductus arteriosus, a major fetal off-target of current tocolytics. A high-throughput combination screen of in vitro intracellular Ca2+-mobilization identified that mundulone exhibits synergism with two clinical-tocolytics (atosiban and nifedipine), and MA displayed synergistic efficacy with nifedipine. Of these synergistic combinations, mundulone + atosiban demonstrated a favorable in vitro therapeutic index (TI)=10, a substantial improvement compared to TI=0.8 for mundulone alone. The ex vivo and in vivo synergism of mundulone and atosiban was substantiated, yielding greater tocolytic efficacy and potency on isolated mouse and human myometrial tissue and reduced preterm birth rates in a mouse model of PL compared to each single agent. Treatment with mundulone 5hrs after mifepristone administration (and PL induction) dose-dependently delayed the timing of delivery. Importantly, mundulone in combination with atosiban (FR 3.7:1, 6.5mg/kg + 1.75mg/kg) permitted long-term management of PL after induction with 30 g mifepristone, allowing 71% dams to deliver viable pups at term (> day 19, 4-5 days post-mifepristone exposure) without any visible maternal and fetal consequences. Collectively, these studies provide a strong foundation for the future development of mundulone as a stand-alone single- and/or combination-tocolytic therapy for management of PL.

pharmacology and toxicology↗

bioRxiv2022

Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift

Cohort-specific 16S rRNA sequence-based studies associating gut microbiota with obesity are often marred with contradictory findings regarding community structure and composition leading to "reproducibility crisis" of the signals. Moreover, taxonomic drivers of the obesity-linked gut microbial functional imbalances and their replicability also remains unexplored which should be useful for in-depth understanding of obese host-gut microbiota interaction and, strategizing therapeutics. We addressed these questions through unbiased meta-analysis and further machine-learning validation of 692 curated fecal whole metagenomic sequence datasets from diverse geographical locations. Further, obesity-linked pathway shifts were traced back to their specific drivers by integrating the species and pathway profiles through genomic content of the species. We found reproducible depletion of diversity in obese gut microbiome without any pattern in Firmicutes/Bacteroidetes ratio. Additionally, we also identified obesity-linked robust and reproducible gut microbial species and pathway features. Contributors of these pathway features identified as both dataset-specific and shared across the datasets.

microbiology↗

bioRxiv2021

High throughput screening of a new fluorescent G-quadruplex ligand having telomerase inhibitory activity in human A549 cells

Genome-wide analysis showed that putative G-quadruplex DNA structures are prevalent in the human genome. The presence of G-quadruplex structure in the telomere and promoter region of certain oncogenes inspired people to use G-quadruplex ligand as anti-cancer agents. G-quadruplex structures, stabilized by ligand at telomere are resolved by telomerase making the cancer cells resistant to G-quadruplex ligand. So, identification of a new G-quadruplex ligand having anti-telomerase activity would be a promising strategy for cancer therapy as about 85% of human cancers are telomerase positive. A set of the drug-like compounds were screened from the ZINC database randomly and 2284 ligands were chosen following Lipinskis rule of five that were docked with five different G-quadruplex DNA sequences in idock. We screened 43 potential G-quadruplex binders using Z-score as a normalization scoring function. The compound (ZINC ID-05220992) gave the best score (average idock = -10.17 kcal/mol, average normalized idock = -3.42). We performed G4 FID assay, CD analysis to understand its binding with three different G-quadruplex DNA sequences, and checked its anti-telomerase activity in A549 cells using TRAP assay. We observed that this compound had an intrinsic fluorescence, capability to stain live cells with a blue fluorescence, and a specific affinity to only 22AG out of three different G-quadruplex DNA sequences under study. It showed cytotoxicity, good permeability to live cells, and a significant reduction of telomerase activity in human A549 cells at a very low dose. So, this compound has strong potential to be an anti-cancer drug. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/470216v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@116cce1org.highwire.dtl.DTLVardef@1e500c1org.highwire.dtl.DTLVardef@194a0b3org.highwire.dtl.DTLVardef@c258fe_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIA set of compounds were screened randomly by a High throughput method and Lipinskis rule of five from ZINC database to identify potential G4-binders. C_LIO_LIThe compound (ZINC ID-05220992) was screened after docking with five G-quadruplex DNA C_LIO_LIIt binds G-quadruplex DNA 22AG as detected by TO displacement and CD spectroscopy. C_LIO_LIIt inhibits telomerase activity in A549 cells and also cytotoxic to this cell. C_LIO_LIIt penetrates live A549 cell in culture and stains it with blue fluorescence C_LI

molecular biology↗

bioRxiv2021

Rheb-mTOR Activation Rescues Amyloid Beta-Induced Cognitive Impairment and Memory Function by Restoring miR-146 Activity in Glial Cells

Deposition of amyloid beta plaques in adult rat or human brain is associated with increased production of proinflammatory cytokines by associated glial cells that are responsible for degeneration of the diseased tissue. The expression of these cytokines is usually under check and is controlled at post-transcriptional level via several microRNAs. Computational analysis of gene expression profiles of cortical regions of Alzheimers disease patients brain suggests ineffective target cytokine mRNA suppression by existing microRNPs in diseased brain. Exploring the mechanism of amyloid beta induced cytokine expression, we have identified how the inactivation of the repressive miR-146 microRNPs causes increased production of cytokines in amyloid beta exposed glial cells. In exploration of the cause of miRNP inactivation, we have noted amyloid beta oligomer induced sequestration of mTORC1 complex to early endosomes that results in decreased Ago2 phosphorylation, limited Ago2-miRNA uncoupling and retarded Ago2-cytokine mRNA interaction in rat astrocyte cells. Interestingly, constitutive activation of mTORC1 by Rheb activator restricts proinflammatory cytokine production by reactivating miR-146 microRNPs in amyloid beta exposed glial cells to rescue the disease phenotype in the in vivo rat model of Alzheimers disease.

neuroscience↗

bioRxiv2020

Amyloid Beta Oligomers Prevents Lysosomal Targeting of miRNP to Stop Its Recycling and Target Cytokine Repression in Glial Cells

mRNAs encoding inflammatory cytokines are targeted by miRNAs and remain repressed in neuroglial cells. On exposure to amyloid beta 1-42 oligomers, glial cells start expressing proinflammatory cytokines although there has been increase in repressive miRNAs levels as well. Exploring the mechanism of this potential immunity of target cytokine mRNAs against repressive miRNAs in amyloid beta exposed glial cells, we have identified differential compartmentalization of repressive miRNAs in glial cells to explain this aberrant miRNA function. While the target mRNAs were found to be associated with polysomes attached to endoplasmic reticulum, the miRNPs found to be present predominantly with endosomes that failed to recycle to endoplasmic reticulum attached polysomes to repress mRNA targets in treated cells. Amyloid beta oligomers, by masking the Rab7 proteins on endosomal surface, affects Rab7 interaction with Rab Interacting Lysosomal Protein (RILP) on lysosomes to restrict endosomal maturation and its lysosomal targeting. This causes retarded miRNP targeting to lysosomes and recycling. Similar defects in miRNP retrieval has been observed in endosome maturation defective cells depleted for RILP or treated with Bafilomycin. RNA processing body localization of the miRNPs was also noted in treated cells that happens as a consequence of enhanced endosomal retention of miRNPs. Interestingly, depletion of P-body partly rescues the miRNA function in glial cells exposed to amyloid beta and restricts the excess cytokine expression there. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/424324v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1d9453dorg.highwire.dtl.DTLVardef@150a9c4org.highwire.dtl.DTLVardef@b99a1aorg.highwire.dtl.DTLVardef@1342676_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIAmyloid beta exposure causes accumulation of inactive miR-146 miRNP to cause elevated proinflammatory cytokine production in glial cells. C_LIO_LIAmyloid beta masks Rab7-RILP interaction to reduce endosome lysosome interaction. C_LIO_LIAccumulated miRNPs failed to get targeted to lysosomes in amyloid exposed cells due to loss of endosome lysosome interaction C_LIO_LILysosomal compartmentalization of miRNPs is required for its recycling and repression of de novo targets C_LIO_LIAccumulated miRNPs are stored in P-Bodies and depletion of P-Bodies rescues miRNA function in amyloid exposed glial cells. C_LI

cell biology↗