Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing

Long-read whole-genome sequencing analysis of DNA methylation would provide useful information on the chromosomal context of gene expression regulation. Here we describe the development of a method that improves the read length generated by using the bisulfite-sequencing-based approach. In this method, we combined recently developed enzymatic base conversion, where an unmethylated cytosine (C) should be converted to thymine (T), with nanopore sequencing. After methylation-sensitive base conversion, the sequencing library was constructed using long-range polymerase chain reaction. This type of analysis is possible using a minimum of 1 ng genomic DNA, and an N50 read length of 3.4–7.6 kb is achieved. To analyze the produced data, which contained a substantial number of base mismatches due to sequence conversion and an inaccurate base read of the nanopore sequencing, a new analytical pipeline was constructed. To demonstrate the performance of long-read methylation sequencing, breast cancer cell lines and clinical specimens were subjected to analysis, which revealed the chromosomal methylation context of key cancer-related genes, allele-specific methylated genes, and repetitive or deletion regions. This method should convert the intractable specimens for which the amount of available genomic DNA is limited to the tractable targets.     

Antioxidative status changes in golden syrian hamsters with experimental metabolic syndrome

Some indices of the antioxidant status (content of the alpha-tocopherol, reduced glutathione and ascorbic acid, activity of the glutathione reductase and aryl-esterase) and lipid peroxidation processes in the liver, blood serum, and some blood serum lipoprotein fractions of the Golden Syrian hamsters of different sex and age status under high-caloric diet were investigated. It has been shown that the hypercaloric diet leads to a decreaseng of reduced glutathione content and increase of the level of lipid peroxidation products in the liver of experimental animals. The ascorbic acids content in male liver is decreased and in female liver is increased. In the blood serum under hypercaloric nutrition the accumulation of lipid peroxidation products and alpha-tocopherol content a decrease in ApoB-lipoproteins and HDL is observed. Simultaneously the ascorbic acid content is increased in the blood serum of all experimental animals. Activation of free-radical oxidation both in the liver, and blood serum is more significant in males compared with females. The data obtained allow to suppose that atherosclerotic complications of metabolic syndrome development may be connected to the lipoprotein oxidant status infringement.     

In vitro segmentation induction of Mesocestoides corti (Cestoda) tetrathyridia

Mesocestoides corti is a suitable model for studying cestode development because of its ability to reproduce asexually and segment in vitro. The cultured parasite is also capable of sexual differentiation and, probably, reproduction. To establish conditions that increase the efficiency of in vitro M. corti larvae (tetrathyridia) segmentation, we tested the effects of an inducing agent and some physical parameters in cultures. We found that a 5% CO2-95% N2 gas phase, an incubation temperature of 39 C (instead of 37 C), and a 24-hr pretreatment with trypsin (10(5) BAEE/ml, BAEE = Na-benzoil-L-arginine ethyl ester unit of trypsin activity) in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 20% fetal bovine serum (FBS) are able to increase individually or synergistically the segmentation rate of tetrathyridia. A segmentation rate of up to 100% was achieved on day 4 of culture, when all these conditions were used simultaneously, in comparison with an average rate of 40% obtained not before day 11 in cultures without any inducing treatment. Fetal bovine serum is essential for segmentation, and a concentration of 20% was established as the standard for induction.     

Antimicrobial activity of two novel coumarin derivatives: 3-cyanonaphtho[1,2-(e)] pyran-2-one and 3-cyanocoumarin

The antimicrobial activity of the two novel coumarin derivatives, 3-cyanonaphthol[1,2-(e)]pyran-2-one and 3-cyanocoumarin was determined. The two novel coumarin derivatives showed specific activity against most gram-positive organisms and yeast with lower activity against most gram-negative bacteria. The MIC values of compounds showed that they are largely active against E. coli to a lesser extent against S. aureus and C. albicans.     

DNA strand scission in E.coli by electronically excited state molecules generated by enzymatic systems

$\text{E.}\text{coli}$ containing pAT 153 plasmid undergoes strand scission when exposed to the indole-3-acetic acid/peroxidase/D₂ system. Neither the initial components of this reaction nor the final stable products are responsible for this effect. Indole-3-aldehyde in its triplet state and singlet oxygen have been recently identified in this system. That singlet oxygen is one of the species acting on the plasmid in $\text{E.}\text{coli}$ cells was suggested by protective effect of histidine and guanosine which are singlet oxygen quenchers. Similar effect on plasmid with malonaldehyde/peroxidase/O₂ system was observed, which is an excellent singlet oxygen generator. This is the first report of a biological system where it is possible to detect a DNA scission in the intact cell by a bioenergized process. This presumably is related to spontaneous mutagenesis.     

Phytochemical Diversity and Pharmacological Properties of Rhus coriaria

Rhus coriaria L. (Anacardiaceae), sumac, is a common condiment, appetizer and souring agent in the Mediterranean region that has a long history in traditional medicine. R. coriaria has been prescribed for the treatment of many ailments including diarrhea, ulcer, hemorrhoids, hemorrhage, wound healing, hematemesis, and eye ailments like ophthalmia and conjunctivitis. The plant is also used as diuresis, antimicrobial, abortifacient and as a stomach tonic. Sumac is known to be rich in different classes of phytochemicals including tannins, polyphenols, flavonoids, organic acids and essential oils and continues to be a hot topic for extensive research work designed for revealing its phytochemical constituents and evaluating its bioactive properties. This review summarizes the recent phytochemical and diverse bioactivity studies on R. coriaria, especially those concerned with antitumor, antioxidant, hypoglycemic, antimicrobial, and anti‐inflammatory studies.     

A conserved role for phosphatidylinositol 3-kinase but not Akt signaling in mitochondrial adaptations that accompany physiological cardiac hypertrophy

Physiological cardiac hypertrophy is associated with mitochondrial adaptations that are characterized by activation of PGC-1alpha and increased fatty acid oxidative (FAO) capacity. It is widely accepted that phosphatidylinositol 3-kinase (PI3K) signaling to Akt1 is required for physiological cardiac growth. However, the signaling pathways that coordinate physiological hypertrophy and metabolic remodeling are incompletely understood. We show here that activation of PI3K is sufficient to increase myocardial FAO capacity and that inhibition of PI3K signaling prevents mitochondrial adaptations in response to physiological hypertrophic stimuli despite increased expression of PGC-1alpha. We also show that activation of the downstream kinase Akt is not required for the mitochondrial adaptations that are secondary to PI3K activation. Thus, in physiological cardiac growth, PI3K is an integrator of cellular growth and metabolic remodeling. Although PI3K signaling to Akt1 is required for cellular growth, Akt-independent pathways mediate the accompanying mitochondrial adaptations.     

Perinatal exposure to low doses of 2,3,7,8-tetrachlorodibenzo-p-dioxin alters sex-dependent expression of hepatic CYP2C11

The cytochrome P450 (CYP) isoform CYP2C11 is specifically expressed in the liver of adult male rats, and 5alpha-reductase is specifically expressed in the liver of the adult female rats. The sexually dimorphic expressions of these hepatic enzymes are regulated by the sex-dependent profiles of the circulating growth hormone (GH). However, it is not well known whether hormonal imprinting or activation factors in the neonatal brain influence the sexually dimorphic expression patterns of hepatic enzymes. We therefore examined the effect of perinatal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on sex-dependent expressions of hepatic enzymes. Pregnant rats were treated with TCDD at a dose of 0, 200, or 800 ng/kg on gestation day 15, exposing the pups to the chemical. Although the expression of CYP2C11 protein in the livers of male pups on postnatal day (PND) 49 was significantly higher than that of the controls, but the 5alpha-reductase activities in the livers of female pups were not altered by exposure to TCDD. Focusing on perinatal periods, testosterone and estrogen levels significantly increased in the brain of male pups on PND 2. The results suggest that the alteration of testosterone and estrogen levels affect hormonal imprinting in the neonatal brain of male pups, and thus induces a change in the level of male-specific hepatic CYP2C11. We conclude that perinatal exposure to TCDD at low doses may change the sexual differentiation of the neonatal brain in male rats.     

Proteomic analysis of the larval stage of the parasite Echinococcus granulosus: causative agent of cystic hydatid disease

We describe the preparation of Echinococcus granulosus metacestode protein extracts for two-dimensional electrophoresis (2-DE). Protoscoleces and hydatid fluid were prepared by precipitation using trichloroacetic acid (TCA) to remove nonprotein contaminants. Compared to the untreated control, TCA precipitation improved the 2-DE gel profile of the protoscoleces proteins. Comparison of 2-DE gels from insoluble and soluble fractions of the protoscoleces protein extract showed that most proteins are insoluble after lysis by sonication. Host serum proteins, especially albumin and globulins, caused horizontal streaking problems on the hydatid fluid 2-DE gels due to their high content in this sample. Even after the preparation of a hydatid fluid parasite enriched fraction, the high amount of bovine serum albumin and globulins made parasite-specific proteins difficult to detect by 2-DE. Despite the absence of an E. granulosus genome sequencing or expressed sequence tag (EST) projects, it was possible to identify 15 prominent protein spots from a whole protein protoscoleces 2-DE gel by peptide mass fingerprinting. These include actins, tropomyosin, paramyosin, thioredoxin reductase, antigen P-29, cyclophilin, and the heat shock proteins hsp70 and hsp20. This work demonstrates that 2-DE and PMF are important tools to identify proteins from the hydatid fluid and protoscoleces and for the comparative analysis of cysts from different hosts or between active and resting cysts.