Flanking sequence preference modulates de novo DNA methylation in the mouse genome

Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.     

Chemotaxonomic evaluation of Turkish species of Salvia: Fatty acid compositions of seed oils

Fatty acid composition of nine species of Salvia, naturally growing in Turkey was determined: Salvia syriaca, Salvia potentillifolia, Salvia candidissima ssp. occidentalis, Salvia macrochlamys, Salvia poculata, Salvia tomentosa, Salvia recognita, Salvia virgata and Salvia ceratophylla. The main compounds were found to be linoleic acid (18:2; 24.3–69.2%), linolenic acid (18:3; 0.6–40.8%), oleic acid (18:1; 8.3–31.0%), palmitic acid (16:0; 3.8–21.0%) and stearic acid (18:0; 1.8–5.2%). Fatty acid composition of Salvia seed oils could be used as a chemotaxonomical marker.     

Double Staining of Skeleton Using Microwave Irradiation

The fetal skeleton double staining method is used to reveal developmental abnormalities in the skeletal system. We used alizarin red S and al-cian blue successfully with microwave irradiation for skeletal double staining. The fixation time was reduced from 4-7 days to 2-2.5 min and the staining time was reduced from 4 days to 23 min.     

Terbinafine hydrochloride loaded liposome film formulation for treatment of onychomycosis: in vitro and in vivo evaluation

Onychomycosis is a fungal infection of nail unit that is caused by dermatophytes. Oral Terbinafine hydrochloride (TBF-HCl) is being used for the treatment of onychomycosis since 24 years. The side effects caused by the systemic application and limitations of topical administration of this drug regarding the diffusion through nail lead to the development of a new formulation based on, TBF-HCl-loaded liposome. The newly obtained film formulations were prepared and characterized via several parameters, such as physical appearance, drug content, thickness, bioadhesive properties and tensile strength. In vitro and ex vivo permeation studies were performed to select an optimum film formulation for antifungal activity to show the efficiency of formulations regarding the treatment of onychomycosis. The in vitro release percentages of drug were found 71.6?±?3.28, 54.4?±?4.26, 56.1?±?7.48 and 46.0?±?2.43 for liposome loaded pullulan films (LI-P, LII-P) and liposome loaded Eudragit films (LI-E, LII-E), respectively. The accumulated drug in the nail plates were found 31.16?±?4.22, 24.81?±?5.35, 8.17?±?1.81 and 8.92?±?3.37 for LI-P, LII-P, LI-E and LII-E, respectively, which within therapeutic range for all film formulations. The accumulated drug in the nail plate was found within therapeutic range for all film formulations. The efficacy of the selected TBF-HCl-loaded liposome film formulation was compared with TBF-HCl-loaded liposome, ethosome, liposome poloxamer gel and ethosome chitosan gel formulations. It was found that TBF-HCl-loaded liposome film formulation had better antifungal activity on fungal nails which make this liposome film formulation promising for ungual therapy of fungal nail infection.     

BAZ2A safeguards genome architecture of ground‐state pluripotent stem cells

Chromosomes have an intrinsic tendency to segregate into compartments, forming long‐distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground‐state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub‐domains within the active A compartment, which intersect through long‐range contacts. We found that ground‐state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A‐dependent manner. Finally, ground‐state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.     

Malondialdehyde, Glutathione, and Nitric Oxide Levels in Toxoplasma gondii Seropositive Patients

The aim of this study was to investigate the difference in the serum malondialdehyde (MDA), glutathione (GSH), and nitric oxide (NO) levels between normal and T. gondii-infected patients. To this end, MDA, GSH, and NO levels in the sera of 37 seropositive patients and 40 participants in the control group were evaluated. In Toxoplasma ELISA, IgG results of the patient group were 1,013.0 ± 543.8 in optical density (mean ± SD). A statistically significant difference was found between patients and the control group in terms of MDA, GSH, and NO levels. A decrease in GSH activity was detected, while MDA and NO levels increased significantly. Consequently, it is suggested that the use of antioxidant vitamins in addition to a parasite treatment shall prove useful. The high infection vs control ratio of MDA and NO levels probably suggests the occurrence as a mechanism of tissue damage in cases of chronic toxoplasmosis. Moreover, it is recommended that the patient levels of MDA, GSH, and NO should be evaluated in toxoplasmosis.     

Identification of NF-κB1 and NF-κBIΑ Polymorphisms Using PCR–RFLP Assay in a Turkish Population

A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) assay was used in a Turkish population to determine the frequency of polymorphisms of the nuclear factor-kappa (NF-κB1) and NF-κBIA genes, which have been shown to be related to several inflammatory diseases and cancer pathogenesis. Total genomic DNA was isolated from peripheral blood samples taken from 565 healthy volunteers living in Ayd?n Province. The genomic regions in question were amplified by PCR, and the polymorphisms in these regions were detected by a PCR–RFLP assay. The frequencies were 10.3% for the NF-κB1 ?94ins/delATTG del/del genotype, 49.1% for del/ins, and 40.6% for ins/ins. The genotype frequencies of the NF-κBIA 3′UTR A → G genotypes were A/A 19.2%, A/G 42.3%, and G/G 38.5%. Distribution of genotype frequencies was tested by Hardy–Weinberg; the NF-κB1 gene was in Hardy–Weinberg equilibrium (χ² = 3.402, P > 0.05), the NF-κBIA gene was not (χ² = 8.293, P < 0.05).