High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Nations within a nation: variations in epidemiological transition across the states of India, 1990–2016 in the Global Burden of Disease Study

18% of the world's population lives in India, and many states of India have populations similar to those of large countries. Action to effectively improve population health in India requires availability of reliable and comprehensive state-level estimates of disease burden and risk factors over time. Such comprehensive estimates have not been available so far for all major diseases and risk factors. Thus, we aimed to estimate the disease burden and risk factors in every state of India as part of the Global Burden of Disease (GBD) Study 2016

Fabrication and Characterization Techniques of In Vitro 3D Tissue Models

The culturing of cells in the laboratory under controlled conditions has always been crucial for the advancement of scientific research. Cell-based assays have played an important role in providing simple, fast, accurate, and cost-effective methods in drug discovery, disease modeling, and tissue engineering while mitigating reliance on cost-intensive and ethically challenging animal studies. The techniques involved in culturing cells are critical as results are based on cellular response to drugs, cellular cues, external stimuli, and human physiology. In order to establish in vitro cultures, cells are either isolated from normal or diseased tissue and allowed to grow in two or three dimensions. Two-dimensional (2D) cell culture methods involve the proliferation of cells on flat rigid surfaces resulting in a monolayer culture, while in three-dimensional (3D) cell cultures, the additional dimension provides a more accurate representation of the tissue milieu. In this review, we discuss the various methods involved in the development of 3D cell culture systems emphasizing the differences between 2D and 3D systems and methods involved in the recapitulation of the organ-specific 3D microenvironment. In addition, we discuss the latest developments in 3D tissue model fabrication techniques, microfluidics-based organ-on-a-chip, and imaging as a characterization technique for 3D tissue models

Biogenic Ceria Nanoparticles (CeO2 NPs) for Effective Photocatalytic and Cytotoxic Activity

Ceria nanoparticles (CeO2 NPs) are generally considered in various functional applications, such as catalysts in fuel cells, sensors, and antioxidant and oxidase-like enzymes in the biological environment. The CeO2 NPs were synthesized using the E. globulus leaf extract-mediated hydrothermal technique. The synthesized NPs were characterized by various analytical instruments including powder X-ray diffractometer (PXRD), scanning electron microscope (SEM), transmission electron microscope (TEM) and dynamic light scattering (DLS) analysis. The XRD results showed an average NPs sizes of 13.7 nm. Cytotoxic study results showed an IC50 value of 45.5 µg/L for A549 and 58.2 µg/L for HCT 116, indicating that CeO2 NPs are more toxic to A549 compared to HCT116 cell lines. The generation of ROS was responsible for its cytotoxic activity against cancer cell lines. Specific surface area (40.96 m2/g) and pore diameter (7.8 nm) were measured using Brunauer–Emmett–Teller (BET) nitrogen adsorption–desorption isotherms. CeO2 NPs with a high surface area were used as photocatalyst in degrading sunset yellow (SY) dye under UV-irradiation and 97.3% of the dye was degraded within 90 min. These results suggest that the synthesized CeO2 NPs could be used as a good photocatalyst as well as a cytotoxic agent against human cancer cell lines

Efficient One-Pot Solvothermal Synthesis and Characterization of Zirconia Nanoparticle-Decorated Reduced Graphene Oxide Nanocomposites: Evaluation of Their Enhanced Anticancer Activity toward Human Cancer Cell Lines.

This study mainly deals with an effective one-pot solvothermal synthetic pathway for the preparation of uniformly dispersed zirconium oxide nanoparticles on the flattened rough surface of reduced graphene oxide (ZrO2/rGO NCs) using the aqueous leaf extract of Andrographis paniculata. After obtaining detailed information on the preparation and characterization, the anticancer activity of the synthesized ZrO2/rGO nanocrystals (NCs) was evaluated on two human cancer cell lines (A549 and HCT116) along with one normal human cell line (hMSC). The 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide assays revealed that ZrO2/rGO NCs exhibited a dose-dependent cytotoxicity pattern. The cell viability (%) drastically decreases up to 96-98% after exposure to an optimal concentration of 10 ppm nanocomposites. Analysis of both the reactive oxygen species generation and the Annexin V-FTIC staining assays reveal that ZrO2/rGO NCs have the ability to induce apoptosis in A549 and HCT116 cell lines. Thus, the green synthesis of ZrO2/rGO NCs shows potential in developing efficient therapeutic agents for cancer therapy

Biofabricated Palladium Nanoparticle-Decorated Reduced Graphene Oxide Nanocomposite Using the Punica granatum (Pomegranate) Peel Extract: Investigation of Potent In Vivo Hepatoprotective Activity against Acetaminophen-Induced Liver Injury in Wistar Albino Rats.

Acute acetaminophen (APAP) toxicity is a predominant clinical problem, which causes serious liver injury in both humans and experimental animals. This study presents the histological and biochemical factor and antioxidant enzyme level changes induced by an acute acetaminophen overdose in Wistar albino rat livers to elucidate the effective hepatoprotective potential of biofabricated palladium nanoparticle-decorated reduced graphene oxide nanocomposites (rGO/PdNPs-NC) compared to silymarin. After detailed characterization of the hepatoprotective potential of the synthesized rGO/PdNPs-NC, the rats were divided into eight groups (n = 6): control group (normal saline, 1 mL/kg b.w.), silymarin, Punica granatum (pomegranate) peel extract, PdNPs, reduced graphene oxide (rGO-PG), and reduced graphene oxide palladium nanocomposites (rGO/PdNPs-NC, low and high doses) for 7 successive days. The acetaminophen (APAP)-treated group was administered a single dose of acetaminophen (2 g/kg b.w.) on the 8th day. The histopathological results showed that the acetaminophen overdose group exhibited massive intrahepatic hemorrhagic necrosis around the centrilobular region with hepatocytes with vacuolization and swollen cytoplasm found in the liver architecture. This hepatopotential was further assessed by various biochemical parameters such as SGOT, SGPT, ALB, ALP, LDH, direct bilirubin, total bilirubin, and total protein. Also, the antioxidant parameters such as SOD, CAT, MDA, GSH, GRD, and GST were assayed. Rats of groups 7 and 8 showed a significant decrease in SGOT, SGPT, ALP, LDH, direct bilirubin, and total bilirubin (p < 0.001), while a significant increase in the final total protein and ALB as compared to group 2 rats (p < 0.001) was observed. The antioxidant parameters exhibited that rats of groups 7 and 8 showed a significant (p < 0.001) increase in the level of SOD, CAT, GSH, GRD, and GST without affecting the MDA as compared to group 2 rats. Also, the hepatoprotective potential of rGO/PdNPs-NC (low and high doses) was comparable to that of the standard reference drug silymarin. The present study reveals that the rGO/PdNPs-NC possesses significant hepatoprotective activity and acts as an effective and promising curative agent against acetaminophen-induced hepatotoxicity

One-Pot Solvothermal Synthetic Route of a Zinc Oxide Nanoparticle-Decorated Reduced Graphene Oxide Nanocomposite: An Advanced Material with a Novel Anticancer Theranostic Approach.

Publication status: PublishedThis study focuses on a one-pot solvothermal synthetic route for the preparation of uniformly decorated zinc oxide nanoparticles on the surface of reduced graphene oxide (rGO/ZnO-NC) by using Andrographis paniculata leaf aqueous extract as an eco-friendly reducing agent. After characterizing the samples by different physical and chemical techniques, the anticancer activity of the synthesized rGO/ZnO-NC was examined on two human cancerous cell lines (HCT116 and A549) and one normal cell line (hMSCs). The MTT assays revealed that rGO/ZnO-NC exhibited dose-dependent cytotoxicity at a maximum concentration range of 10 ppm and the viability of the cells was drastically decreased to 95-96%. Measurement of reactive oxygen species (ROS) generation and Annexin V-FTIC staining assay revealed that rGO/ZnO-NC induced apoptosis in HCT116 and A549 cell lines. Thus, this study shows that the green-synthesized rGO/ZnO-NC has great potential in developing an efficacious novel therapeutic agent for cancers