Metal nanoparticles (AgNPs and ZnONPs) were synthesized using a green methodology with the green leaves extract of the Bedu (Ficus palmata) tree as a reducing agent and the support of natural fibers. ...The synthesized AgNPs and ZnONPs were characterized by several techniques, including ultraviolet–visible spectral analysis, powder X-ray diffraction crystal analysis, scanning electron microscopy, EDAX, transmission electron microscopy, and Fourier transform infrared spectroscopy, which confirmed that the synthesized particles are in the nano range (1–100 nm), i.e., 30 nm for AgNPs with polydispersity and a spherical shape, whereas the average size of synthesized ZnONPs is 34 nm and they seem to exhibit a distorted spherical shape. The results of thermogravimetric analysis confirmed a weight loss of 18.02% for AgNPs under exothermic conditions due to the desorption of water, and ZnONPs show weight loss between 265 and 500 °C. Both synthesized MNPs are highly thermally stable. Anti-inflammatory and anti-diabetic studies of metal NPs have been evaluated. The AgNPs and ZnONPs of F. palmata leaves showed remarkably highly potent activity for respective strains. In vitro anti-diabetic activity was found for inhibition of α-amylases and α-glucosidases by synthesized silver nanoparticles.
A major fraction of the transcriptome of higher organisms comprised an extensive repertoire of long non-coding RNA (lncRNA) which express in a cell type and development stage-specific manner. While ...lncRNAs are a proven component of epigenetic gene expression modulation, epigenetic regulation of lncRNA itself remains poorly understood. Here we have analysed pan-genomic DNA methylation and histone modification marks (H3K4me3, H3K9me3, H3K27me3 and H3K36me3) associated with transcription start site (TSS) of lncRNA in four different cell types and three different tissue types representing various cellular stages. We observe that histone marks associated with active transcription H3K4me3 and H3K36me3 along with the repressive histone mark H3K27me3 have similar distribution pattern around TSS irrespective of cell types. Also, the density of these marks correlates well with expression of protein-coding and lncRNA genes. In contrast, the lncRNA genes harbour higher methylation density around TSS than protein-coding genes regardless of their expression status. Furthermore, we found that DNA methylation along with the other repressive histone mark H3K9me3 does not seem to play a role in lncRNA expression. Thus, our observation suggests that epigenetic regulation of lncRNA shares common features with mRNA except the role of DNA methylation which is markedly dissimilar.
3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction ...with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these methods required abundant starting material (>500,000 cells), sizable number of sequencing reads (>100 million reads), and elaborate data processing methods to reduce background noise, which limited their use in primary cells. Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT) is a new transposase-assisted tagmentation method that generates high-resolution protein directed long-range chromatin interactions as efficiently as existing methods, HiChIP and ChIA-PET, despite using 100,000 cells (5-fold less) and 12 million sequencing reads (8-fold fewer). Moreover, HiCuT generates high resolution fragment libraries with low background signal that are easily interpreted with minimal computational processing. We used HiCuT in human primary skin cells to link previously identified single nucleotide polymorphisms (SNPs) in skin disease to candidate genes and to identify functionally relevant transcription factors in an unbiased manner. HiCuT broadens the capacity for genomic profiling in systems previously unmeasurable, including primary cells, human tissue samples, and rare cell populations, and may be a useful tool for all investigators studying human genetics and personalized epigenomics.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Vitamin B
12
deficiency is a critical problem worldwide and peri-conceptional deficiency of this vitamin is associated with the risk of complex cardio-metabolic diseases. Nutritional perturbations ...during these stages of development may lead to changes in the fetal epigenome. Using Wistar rat model system, we have earlier shown that low maternal B
12
levels are associated with low birth weight, adiposity, insulin resistance, and increased triglyceride levels in the offspring, which might predispose them to the risk of cardio-metabolic diseases in adulthood. In this study, we have investigated the effects of maternal B
12
deficiency on genome-wide DNA methylation profile of the offspring and the effect of rehabilitation of mothers with B
12
at conception. We have performed methylated DNA immunoprecipitation sequencing of liver from pups in four groups of Wistar rats: Control (C), B
12
-restricted (B
12
R), B
12
-rehabilitated at conception (B
12
RC), and B
12
-rehabilitated at parturition (B
12
RP). We have analyzed differentially methylated signatures between the three groups as compared to controls. We have identified a total of 214 hypermethylated and 142 hypomethylated regions in the 10 kb upstream region of transcription start site in pups of B
12
-deficient mothers, which are enriched in genes involved in fatty acid metabolism and mitochondrial transport/metabolism. B
12
rehabilitation at conception and parturition is responsible for reversal of methylation status of many of these regions to control levels suggesting a causal association with metabolic phenotypes. Thus, maternal B
12
restriction alters DNA methylation of genes involved in important metabolic processes and influences the offspring phenotype, which is reversed by B
12
rehabilitation of mothers at conception.
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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact ...within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencing-based approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the three-dimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.
Balanced structural variants are mostly described in disease with gene disruption or subtle rearrangement at breakpoints.
Here we report a patient with mild intellectual deficiency who carries a de ...novo balanced translocation t(3;5). Breakpoints were fully explored by microarray, Array Painting and Sanger sequencing. No gene disruption was found but the chromosome 5 breakpoint was localized 228-kb upstream of the MEF2C gene. The predicted Topologically Associated Domains analysis shows that it contains only the MEF2C gene and a long non-coding RNA LINC01226. RNA studies looking for MEF2C gene expression revealed an overexpression of MEF2C in the lymphoblastoid cell line of the patient.
Pathogenicity of MEF2C overexpression is still unclear as only four patients with mild intellectual deficiency carrying 5q14.3 microduplications containing MEF2C are described in the literature. The microduplications in these individuals also contain other genes expressed in the brain. The patient presented the same phenotype as 5q14.3 microduplication patients. We report the first case of a balanced translocation leading to an overexpression of MEF2C similar to a functional duplication.
An elevated level of thiol amino acid homocysteine is associated with several complex disorders. Homocysteine ability to bind proteins, thereby modulating their structure and function, is proposed to ...be one of the mechanisms of homocysteine induced pathogenecity. Homocysteine and homocysteine thiolactone bind to protein cysteine and lysine residues respectively. A major hurdle in studying protein homocysteinylation is the lack of suitable analytical techniques to determine simultaneously the concentrations of reduced and oxidized forms of homocysteine and cysteine (especially homocysteine–cysteine mixed disulfide) together with thiolactone formed during the reaction of homocysteine or thiolactone with proteins. Herein we report a capillary electrophoresis method to determine simultaneously the levels of these intermediates. For this 40
mmol/L Tris phosphate buffer at (pH 1.60) was used as running electrolyte, and the separation was performed by the simultaneous application of a CE voltage of 15
kV and an overimposed pressure of 0.1
psi. A rapid separation of these intermediates in less than 6
min with a good reproducibility of both peak areas (CV
<
2%) and migration time (CV
<
0.2%) was obtained. The applicability of our method was validated by incubating reduced homocysteine and albumin and measuring the reaction intermediates in the solution mixture.
A novel acetylated triterpene bisdesmoside saponin is elucidated as named Hederagenin 3-O-α-L-rhamnopyranosyl (3→1)-2,4-O-diacetyl-α-L-arabinopyranosyl-28-O-β-D-glucopyranosyl-(2→1) ...3-O-acetyl-β-D-glucopyranosyl ester (1) along with two known saponins, hederagenin 3-O-(α-L-arabinopyranoside-(1→3)-α-L-rhamnopyranosyl-(1→2)-α-L-arabinopyranoside (2) and hederagenin 3-O-β-D-xylopyranosyl-(1→3)-α-L-rhamnopyranosyl-(1→2)-α-L-arabinopyranoside (3), from the pericarps of Sapindus mukorossi. The structures of these saponins were characterized by means of chemical and spectral methods including advanced 2D NMR studies.
Fig.2. Schematic illustration for the synthesis of Ag-MgO nanocomposite.
Display omitted
•Nanocomposite, reduction catalyst, antioxidant, Citrus aurantium.
In this research article, the bio-synthesis ...of Ag-MgO NCs were synthesized by employing peels extract as a renewable, mild reducing, and stabilizing agent. Bio-synthesized Ag-MgO NCs was characterized by different spectroscopic methods like UV–visible spectroscopy, XRD, SEM, EDX, and TEM. In UV spectra of the nanocomposite, two peaks were obtained at 342 nm and 290 nm for Ag and MgO respectively, during the synthesis of Ag-MgO nanocomposite. The characteristic peak for Ag shows a hypsochromic (blue) shift from 465 nm to 342 nm. XRD results show that the synthesized NCs are cubic in nature considering both Ag-NPs and MgO-NPs and the average crystal size was found to be 16.40 nm. SEM images confirm that the synthesized Ag-MgO NCs are poly dispersive and crystalline in nature. The catalytic activity of Ag-MgO NCs was examined by reduction of toxic dyes such as methylene blue (MB), Rose Bengal (RB), and acridine orange (AO) by using NaBH4 as a reducing agent and NCs as a catalyst. The synthesized Ag-MgO NCs exhibits enhanced catalytic reduction of dyes up to 89.77%, 83.38%, and 87.34% in 7 min, 4 min, and 5 min for MB, RB, and AO respectively. Antioxidant activity of synthesized Ag-MgO nanocomposite was determined by H2O2 free radical scavenging activity, and DPPH free radical scavenging activity. On the premises of our findings the synthesized NCs can be considered as excellent catalyst for degradation of mentioned toxic dyes, Further, these Ag-MgO can act as an efficient antioxidant based on their activity comparable to butylated hydroxy toluene (BHT).
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