Otofaciocervical syndrome (OFCS) is an autosomal recessively inherited disorder characterized by facial dysmorphism, external ear anomalies with preauricular pits and hearing impairment, branchial cysts or fistulas, anomalies of the vertebrae and the shoulder girdle, and mild intellectual disability. In a large consanguineous family with OFCS from Turkey, we performed whole-exome sequencing (WES) of a single pooled DNA sample of four affected individuals. Filtering for variants with a percentage of alternate reads ≥ 90 % and a coverage of at least five reads identified only a single novel homozygous variant, c.497G>T, located in PAX1 that co-segregated with the disease in the family. PAX1 encodes a transcription factor with a critical role in pattern formation during embryogenesis in vertebrates. The mutation is predicted to substitute the glycine at position 166 to valine (p.G166V) within the highly conserved paired-box domain of the PAX1 protein. We performed a dual luciferase reporter assay to examine the transactivation of a regulatory sequence in the Nkx3-2 promoter region, which is a direct target of mouse Pax1 transcriptional regulation. We observed a significantly reduced transactivation in HEK293T cells overexpressing Pax1(G157V) in comparison to Pax1(WT) expressing cells, indicating a reduced DNA-binding affinity of the mutant protein. Taken together, our results show that the strategy of pooling DNA is a powerful, cost-effective application for WES in consanguineous families and establish PAX1 as a new disease-causing gene for OFCS and as part of the EYA-DACH-SIX-PAX network, important in early embryogenesis.

A total of 28 different plants from different regions of Ç anakkale, Turkey, were investigated for their antioxidant capacity and total phenol contents to find new potential sources of natural antioxidants. The antioxidant capacity of methanolic extracts prepared from various parts of plants was evaluated by both trolox equivalent antioxidant capacity (TEAC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays, while the total phenolics were determined using the Folin-Ciocalteu method. The TEAC values of plant extracts ranged in a large scale from 1472.36 to 17.61 lmol of trolox equivalents per g dry weight (dw), and EC 50 values (concentration at which 50% radical scavenging occurred) varied from 0.174 to 42.475 mg dw of plant, while the total phenol content of plant extracts ranged between 117.20 and 1.27 mg of gallic acid equivalents per g dw. There was a positive linear correlation between the TEAC and total phenols of plant materials (r = 0.916). The extracts of Hypericum perforatum, Arbutus andrachne and Paliurus spina-christii showed higher antioxidant activities (both TEAC and DPPH assays). However, there was no clear relationship between TEAC and EC 50 values (r = 0.477) of plant extracts.

Danışman G., Arslan E., Toklucu A.K. (2015): Kinetic analysis of anthocyanin degradation and polymeric colour formation in grape juice during heating. Czech J. Food Sci., 33: 103-108.The degradation of total monomeric anthocyanins and changes in the proportion of polymeric colour (% PC) as well as antioxidant capacity of grape juice were studied during heating at 70-90°C. Anthocyanin degradation fitted to a first order reaction model, while the formation of % PC followed zero order reaction kinetics. High correlations (r = 0.989-0.997) were found between anthocyanin degradation and % PC formation during heating. The activation energies for the degradation of anthocyanins and formation of % PC were 64.89 and 50.42 kJ/mol, respectively. Trolox equivalents antioxidant capacity (TEAC) values of grape juice slightly changed during heating.

In this study, the most commonly used herbicide, glyphosate, was investigated for its genotoxic effects on the genome of Triticum aestivum. Five different concentrations of the herbicide were used, and alterations to DNA were measured quantitatively based on their RAPD (Randomly Amplified Polymorphic DNA) profiles. The genomic template stability (GTS%) at each concentration was evaluated, and a decrease was observed with increasing glyphosate concentration. Thus the highest concentration was concluded to be the most effective for causing alteration to DNA. Additionally, the coupled restriction enzyme digestion-random amplification (CRED-RA) technique was used to determine an epigenetic mechanism, e.g. DNA methylation. The polymorphic percentages of all concentration were calculated after herbicide applications. When in glyphosate doses compared with control group, all applications of glyphosate observed to consist of methylation. The methylation levels range from 28.3 to 73.9 % (DNA hypermethylation). In conclusion, based on the RAPD and CRED-RA results, glyphosate causes DNA alterations and methylation.

Conditions of environmental stress are known to lead genetic and epigenetic variability in plants. DNA methylation is one of the important epigenetic mechanisms and plays a critical role in epigenetic control of gene expression. Thus, the aim of the study was to investigate the alteration of genome methylation induced by zinc stress by using coupled restriction enzyme digestion-random amplification (CRED-RA) technique in maize (Zea mays L.) seedlings. In addition, to determine the effect of zinc on mitotic activity and phytohormone level, high-pressure liquid chromatography (HPLC) and mitotic index analysis were utilized. According to the results, mitotic index decreased in all concentrations of zinc except for 5 mM dose and chromosome aberrations such as c-mitosis, stickiness, and anaphase bridges were determined. It was also observed that increasing concentrations of zinc caused an increase in methylation patterns and decrease in gibberellic acid (GA), zeatin (ZA), and indole acetic acid (IAA) levels in contrast to abscisic acid (ABA) level. Especially increasing of ABA levels under zinc stress may be a part of the defense system against heavy metal accumulation in plants.

No abstract

Dicamba is one of herbicides used widely in agriculture today. The wide use of dicamba in agriculture represents a potential danger to the ecosystems and the environment. Thus, the present study is aimed to investigate the DNA damage levels and the DNA methylation changes in Phaseolus vulgaris subjected to whether dicamba and humic acids (HAs) have any protective effect on these changes. Randomly Amplified Polymorphic DNAs (RAPDs) and Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RAs) were used to determinate the DNA damage levels and the changes in the pattern of DNA methylation. The results showed that dicamba (0.2, 0.4 and 0.6 ppm) caused RAPDs profile changes (DNA damage) as increasing, genomic template stability (GTS) as decreasing and DNA hypomethylation. However, these effects of dicamba seen at higher levels decreased after treatment with five different concentrations (2, 4, 6, 8 and10%) of HAs. The results of this experiment have clearly shown that HAs could be used effectively to protect bean seedlings from the destructive effects of dicamba.

Because the genotype and allele frequency of both polymorphisms are identical, it is most likely that IL1β-511C>T and IL1RN VNTR polymorphisms do not play a role in the development of KC in the Turkish population.