Impact of Chromatin Structures on DNA Processing for Genomic Analyses

Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP) experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome

Length-weight relationships for 30 demersal fish species from çandarli bay (North aegean sea, Turkey) [Duzinsko-maseni odnos za 30 prid-nenih vrsta riba iz zaljeva çandari (sjeverno egejsko more, Turska)]

Length-weight relationships were investigated for 30 demersal fish species from Çandarlı Bay in the North Aegean Sea. Fish samples were caught from depths of 30-95 m in five different stations by bottom trawl between March 2003 and August 2004. The b values in the length-weight relationship varied  between  1.654  and  3.977,  over  50%  of  which  between  2.968  and 3.265 with a mean value of 2.949 (SE = ±0.05). The growth type was determined by t-test: 13 species (43%) showed positive allometries (b > 3; t-test, P 0.05) and the  remaning 4 species (14%) negative allometries (b<3; t-test, P < 0.05). © The Author(s) 2015. Published by University of Zagreb, Faculty of Agriculture. All rights reserved

First record of Epigonus constanciae (Giglioli, 1880), (deepwater cardinalfish) (Osteichthyes: Epigonidae), from Aegean Sea, Turkey

Background. Five specimens of Epigonus constanciae (Giglioli, 1880) (deepwater cardinalfish) were captured first time during a bottom trawl survey in Sigacik Bay and off Karaburun, Aegean Sea. This is the first record of the species from the Aegean Sea. A short description certain of morphometric and meristic features of specimens are given

Gut contents and feeding habits of the great pipefish, syngnathus acus linnaeus, 1758, in İzmir bay (aegean sea, turkey): (Osteichthyes: Syngnathidae)

A total of 112 stomachs of the Great Pipefish, Syngnathus acus Linnaeus, 1758 (56 females and 38 males), was collected in İzmir Bay (Aegean Sea) and analysed in order to determine the feeding habits. 95 specimens (85.6%) were found with prey items in their stomachs. Zooplanktonic organisms were the main food and in terms of numerical (NO%) and frequency (FO%) of occurrence, four main prey categories were determined in the gut content of this species. The most dominant group was found to be harpacticoid copepods (33.6% NO; 57.7% FO), followed by Amphipoda (22.3% NO; 38.2% FO), cypris larvae (12.8%NO; 21.9%FO) and decapod crustaceans (9.5% NO; 16.3% FO), respectively. The numbers of their occurrence indicated that there were significant differences between the seasons. Seasonal differences in the gut content were found in 9 prey groups in spring (p0.05). Consequently, small crustaceans were the most important prey to be consumed in all seasons by all size groups of Syngnathus acus, whereas decapod crustacean larvae/eggs, larger prey items, were preferred by larger specimens. © 2010 Taylor & Francis Group, LLC

Effect of Chip Amount on Microstructural and Mechanical Properties of A356 Aluminum Casting Alloy

Aluminum casting alloys are widely used in especially automotive, aerospace, and other industrial applications due to providing desired mechanical characteristics and their high specific strength properties. Along with the increase of application areas, the importance of recycling in aluminum alloys is also increasing. The amount of energy required for producing primary ingots is about ten times the amount of energy required for the production of recycled ingots. The large energy savings achieved by using the recycled ingots results in a significant reduction in the amount of greenhouse gas released to nature compared to primary ingot production. Production can be made by adding a certain amount of recycled ingot to the primary ingot so that the desired mechanical properties remain within the boundary conditions. In this study, by using the A356 alloy and chips with five different quantities (100% primary ingots, 30% recycled ingots + 70% primary ingots, 50% recycled ingots + 50% primary ingots, 70% recycled ingots + 30% primary ingots, 100% recycled ingots), the effect on mechanical properties has been examined and the maximum amount of chips that can be used in production has been determined. T6 heat treatment was applied to the samples obtained by the gravity casting method and the mechanical properties were compared depending on the amount of chips. Besides, microstructural examinations were carried out with optical microscopy techniques. As a result, it has been observed that while producing from primary ingots, adding 30% recycled ingot to the alloy composition improves the mechanical properties of the alloy such as yield strength and tensile strength to a certain extent. However, generally a downward pattern was observed with increasing recycled ingot amount

Periodic monitoring of persistent organic pollutants and molecular damage in Cyprinus carpio from Büyük Menderes River

PubMed ID: 26081778Concentrations of persistent organic pollutants (POPs) were quantified in river water and sediment, as well as in the liver and muscle tissues of Cyprinus carpio that were sampled four times in a year at three stations in the Büyük Menderes River (BMR). Potential biomarkers of possible cellular molecular damage, namely lipid peroxidation (LPO) degradation products, protein carbonyls (PCO) and DNA repair product 8-hydroxy-2'-deoxyguanosine (8-OHdG), were analysed. All the targeted pollutants were measurable both in biotic and abiotic samples. Interestingly, the results suggested that there was recent organochlorine pesticide (OCP) input into the river water in the first two sampling periods in all stations in contrast to prohibition, while input of polychlorinated biphenyls (PCBs) and polybrominated diphenylethers (PBDEs) was not detected. Liver POP concentrations were higher than in muscle, as expected, and were found to decrease from the first to the fourth sampling period in all stations, except PBDEs. Levels of LPO degradation products in the liver and in muscle tissues decreased from the first to the fourth sampling period. This suggests that these markers reflect the lipid damage in respective tissues due to the tissue burden of targeted POPs. Protein carbonyls were the highest in the first sampling period, followed by a dramatic decrease in the second, and then a gradual increase towards the fourth sampling period in all stations. 8-OHdG levels were lower in Sarayköy station in the first sampling period. Among the measured biomarkers, only several LPO degradation products were significantly correlated with OCPs and PCBs in liver tissue. © 2015, Springer-Verlag Berlin Heidelberg