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Dhara, S.

Publications and source records attributed to Dhara, S..

7 recordsLinked to original sources

Remodeled cephalic arch geometry promotes disturbed flow at pre-maturation flow rates in hemodialysis patients

In the United States, roughly 550,000 people receive routine hemodialysis for end-stage renal disease. This treatment requires an arteriovenous access, most commonly a brachiocephalic fistula. However, these accesses often fail due to stenosis in the cephalic arch (CA), a common complication whose underlying causes remain unclear (Bennet et al., 2015). To characterize the hemodynamic environment in the CA, we employed patient-specific millifluidic models that were perfused with blood-mimicking fluid containing fluorescently labelled beads to visualize flow behaviors. We perfused our models across physiologic (28-45 mL/min) and elevated (60-423 mL/min) flow rates and quantified wall shear stress (WSS) and streamline angle as a measure of flow disturbance. Our findings show that the bulk curvature and remodeled wall topography each create regions of persistently low WSS, consistent with prior clinical observations (Hammes et al., 2016). Moreover, remodeled wall topography promotes disturbed flow at elevated flow rates, a hemodynamic profile associated with various vascular pathologies (Chiu & Chien, 2011). Independently performed computational fluid dynamics (CFD) modeling complements these results, showing that remodeled wall topography promotes vortex formation at elevated flow rates, as assessed by Q-criterion. Collectively, our experimental and computational results provide strong evidence for geometry-driven disturbed flow in the CA at elevated flow rates. Notably, we observed disturbed flow at flow rates as low as 81 mL/min, far below the 600 mL/min required for hemodialysis. Disturbed flow thus offers a plausible mechanism that relates access flow rates to the vascular pathologies that precede access failure. Significance StatementHemodialysis requires an arteriovenous fistula (AVF) that must remodel and mature to withstand chronically elevated blood flow rates. However, how remodeled vessel geometry interplays with elevated flow to shape local hemodynamics remains poorly understood. Here, we used millifluidic models of the cephalic arch (CA) to show that vessel geometry and elevated flow rates promote regions of low wall shear stress and disturbed flow. Notably, geometry-driven disturbed flow is observed at flow rates above physiologic levels but well below 600 mL/min, the flow rate necessary for adequate dialysis. Because disturbed flow is injurious to the endothelium, our findings are the first to show that vascular damage begins before fistula maturation.

biophysics↗

Single-Cell RNA Sequencing Reveals the Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment

The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. We performed single-cell RNA sequencing on freshly collected human PDAC samples either before or after chemotherapy. Overall, we found a heterogeneous mixture of basal and classical cancer cell subtypes, along with distinct cancer-associated fibroblast and macrophage subpopulations. Strikingly, classical and basal-like cancer cells exhibited similar transcriptional responses to chemotherapy, and did not demonstrate a shift towards a basal-like transcriptional program among treated samples. We observed decreased ligand-receptor interactions in treated samples, particularly TIGIT on CD8+ T cells and its receptor on cancer cells, and identified TIGIT as the major inhibitory checkpoint molecule of CD8+ T cells. Our results suggest that chemotherapy profoundly impacts the PDAC TME and may promote resistance to immunotherapy.

cancer biology↗

Hydrothermal Synthesis of Clove Buds-Derived Multifunctional Carbon Dots Passivated with PVP- Antioxidants, Catalysis, and Bioimaging Applications

The present study reports a one-step synthesis of PVP-passivated clove buds derived carbon dots (PPCCDs) using clove buds and polyvinylpyrrolidone (PVP) as the starting precursors via the hydrothermal route. The adopted technique is facile and environmentally friendly for the production of carbon dots (CDs) with in situ PVP passivation. The study evidenced the significant modulation in optical properties of passivated CDs as compared to non-passivated ones. Structural and morphological studies evidenced the spherical PPCCDs with a diameter of [~] 2 nm and crystalline in nature with an interlayer spacing of 0.33 nm. The PPCCDs showed excellent antioxidant activity against DPPH and superoxide anion radicals and also showed good catalytic activity for the degradation of Rhodamine-B (Rh-B) dye under the studied conditions. Their bioimaging potential was evidenced through live-cell fluorescent imaging with 3T3 and L929 cell lines.

cell biology↗

Decellularized micro-scaffolds as stem cell carriers for regeneration of cartilage defects

Cartilage regeneration remains a great challenge in orthopedic treatment owing to their avascular in nature and lack of self-healing ability. Various clinical treatment options are widely used including osteochondral graft transplantation, micro-fracture, blood clot formation and tissue debridement to recover the damaged cartilage. In this circumstance, cartilage defect recovery via tissue engineered functional micro tissue delivery is becoming an emerging trend in musculoskeletal therapeutics. In this study, functional micro-scaffolds (MS) were generated from Capra ear cartilage, and were separated into size-wise groups. The scaffolds were decellularized via NaOH treatment. The cell adhesion study indicated that Capra adipose tissue derived mesenchymal stem cells (ADMSCs) adhesion is more in ~100 m MSs in comparison to 150-300 m MSs. It may be assumed that the cells are compatible to grow on fibrous surface area (100 m) in comparison to dense surface (150-300 m). Further, 100 m MSs were transformed into functional micro tissues (FMTs) in presence of high density ADMSCs in a hanging droplet culture system. The FMTs was transferred to F127 block polymer hydrogel for 3D culture. After 21 d cultures, the FMT clusters were evaluated for quantitative gene expression. To assess the in vivo cartilage defect regeneration potential, FMTs were delivered to rabbit auricular cartilage defect for 15, 30 and 60 d studies. The H&E-stained histological analysis showed that the cartilage defect is almost healed in 60 d study in comparison to 15 and 30 d study.

bioengineering↗

Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility

We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenocarcinoma (PDAC) by ATAC-seq on EpCAM+ PDAC malignant epithelial cells, sorted from 54 freshly resected human tumors, and discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identified two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further developed a novel chromatin accessibility microarray methodology termed "ATAC-Array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this novel methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validated ATAC-array technology in both the original ATAC-Seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a novel, lowcost, clinically feasible technology for assessing chromatin accessibility profiles.

cancer biology↗

Cellular internalization of Godanti Bhasma (anhydrous CaSO4) induces massive cytoplasmic reversible vacuolation and survival response of mammalian cells.

Bhasmas are Ayurvedic herbo-mineral formulations that have been used since ancient times for therapeutic benefits. Godanti Bhasma (GB) is an anhydrous calcium sulfate preparation processed by heating of gypsum powder with herbal extracts. Thermo-transformation of gypsum into the anhydrous GB was confirmed by Raman and FT-IR spectroscopy. GB particle showed size range of 0.5-5 {micro}m and neutral surface charge. Exposure to mammalian cells with GB particles showed massive vacuolation in their cytoplasm. Interestingly, no vacuolation was observed with parent gypsum particle. The result indicated that the cytoplasmic vacuolation by GB was due to its unique physicochemical property obtained during the thermo-transformation of gypsum. Using lysosomal inhibitors Bafilomycin A1 (BFA1) and Chloroquine (CQ), the process of vacuole formation was suppressed indicating GB induced vacuolation require acidic environment. The GB induced vacuolation was also found to follow dose and time dependent manner. Vacuolation often accompany with the sign of cell death whereas, in our study, massive vacuolation by GB did not induce any cell death. Moreover, GB treated cells survive with massive vacuolar process, which was reversed following post-treatment with vacuole inhibitors in GB treated cells, suggesting normal vacuolar function is essential for cell survival. Treatment of cells with GB was also found to induce translocation of LC3 protein from the nucleus to vacuolar membrane, indicating LC3 associated phagocytosis (LAP) is involved in the vacuolar process. Interestingly, the LAP function was found to be reversed in the cells treated with vacuole inhibitors. Our results provide a mechanistic correlation with GB induced vacuolation and associated LAP function, essential for cell survival. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/930594v3_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@169ed89org.highwire.dtl.DTLVardef@169c339org.highwire.dtl.DTLVardef@900004org.highwire.dtl.DTLVardef@1f13823_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility

Time-course high-throughput assays of gene expression and enhancer usage in zebrafish provide a valuable characterization of the dynamic mechanisms governing gene regulatory programs during CNS axon regeneration. To facilitate the exploration and functional interpretation of a set of fully-processed data on regeneration-associated temporal transcription networks, we have created an interactive web application called Regeneration Rosetta. Using either built-in or user-provided lists of genes in one of dozens of supported organisms, our web application facilitates the (1) visualization of clustered temporal expression trends; (2) identification of proximal and distal regions of accessible chromatin to expedite downstream motif analysis; and (3) description of enriched functional gene ontology categories. By enabling a straightforward interrogation of these rich data without extensive bioinformatic expertise, Regeneration Rosetta is broadly useful for both a deep investigation of time-dependent regulation during regeneration in zebrafish and hypothesis generation in other organisms.

genomics↗