Detecting biomarkers with microdroplet technology

The efficient analysis and noninvasive detection of molecules such as DNA, mRNA, and miRNA for clinical diagnostics requires sensitive, high-throughput methods. By segregating individual sequences within separate compartments, digital procedures allow identification of very rare sequences. These procedures are based on the limiting dilution of biological samples in individual compartments such as droplets of a water-in-oil emulsion, and relies on the discrete counting of a given event, providing an absolute value and quantitative data. Coupled with microfluidic systems, digital procedures could become an essential diagnostic tool for the study of diseases as well as patient management.     

Gender Difference in the Influence of Antioxidants on the Blood–Brain Barrier Permeability During Pentylenetetrazol-Induced Seizures in Hyperthermic Rat Pups

Our purpose in this study was to investigate the protective effects of selenium and vitamin E on the blood–brain barrier (BBB) permeability in rats with convulsion under hyperthermic conditions. To eliminate the effect of sex on BBB, we performed our study on 4- to 5-week-old prepubertal rat pups. Evans-blue was used as a BBB tracer. Convulsions were induced by administration of i.p. pentylenetetrazol. In the selenium group, 4 ppm selenium was added to the drinking water for 4–5 weeks. Vitamin E was administered at 700 mg/kg ip. It was shown that the convulsions, both under normothermic and hyperthermic conditions, caused widespread increase in the BBB permeability (p < 0.05). In addition, a significant difference was observed among female and male rats (f [1, 102] = 6.387, p < 0.05). In convulsions under normothermic conditions, there was a further increase in the BBB permeability (F[3, 102] = 43.534, p < 0.001) and a greater increase of permeability in males compared to females (F[1, 102] = 6.387, p < 0.05). Selenium and vitamin E significantly decreased the BBB destruction caused by convulsions under hyperthermic conditions in males (p < 0.05). Treatment with selenium or vitamin E has beneficial effects on the BBB breakdown during convulsions. But gender differences are very important in BBB permeability under pathological conditions and antioxidant treatments.     

Sildenafil is a strong activator of mammalian carbonic anhydrase isoforms I–XIV

Sildenafil citrate, a phosphodiesterase-5 (PDE5) inhibitor widely used for the treatment of erectile dysfunction was investigated for its interaction with the zinc-enzyme carbonic anhydrase (CA, EC 4.2.1.1), as it has in its molecule a piperazine moiety also found in some CA activators (CAAs). Sildenafil was a potent, low micromolar activator of several CA isozymes, such as CA I, VA and VI (K_As in the range of 1.08–6.54 μM), and activated slightly less the isoforms CA III, IV and VA (K_As of 13.4–16.8 μM). CA isozymes II, IX, XIII and XIV showed activation constants in the range of 27.5–34.0 μM, whereas the least activated isoforms were CA VII and XII (K_As of 72.9–73.0 μM). Sildenafil citrate was also given orally to Sprague-Dawley rats at 1 mg/kg body weight. Red blood cell CA activity was inhibited in the treated animals at 3–5 h post-administration (in the range of 60–85%), probably due to NO/nitrite formed by PDE5 inhibition or by another, unknown mechanism. Whether CA activation by sildenafil has clinical consequences in humans is beyond the scope of the present work and warrants further studies.     

Bioremediation potential of a widespread industrial biowaste as renewable and sustainable biosorbent for synthetic dye pollution

In this study, a model synthetic azo dye (Basic red 46) bioremoval by Carpinus betulus sawdust as inexpensive, eco-friendly, and sustainable biosorbent from aqueous solution was examined in a batch biosorption system. The effective environmental parameters on the biosorption process, such as the value of pH, amount of biosorbent, initial dye concentration and contact time were optimized using classical test design. The possible dye-biosorbent interaction was determined by Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy (SEM). The equilibrium, thermodynamic, and kinetic studies for the biosorption of Basic red 46 onto the sawdust biomass were performed. In addition, a single-stage batch dye biosorption system was also designed. The dye biosorption yield of biosorbent was significantly influenced by the change of operating variables. The experimental data were best described by the Freundlich isotherm model and both the pseudo-first-order kinetic and the pseudo-second-order kinetic models. Thermodynamic research indicated that the biosorption of dye was feasible and spontaneous. Based on the Langmuir isotherm model, the biosorbent was found to have a maximum biosorption potential higher than many other biosorbents in the literature (264.915?mg g^?1). Thus, this investigation presents a novel green option for the assessment of waste sawdust biomass as a cheap and effective biosorbent material.     

RNA cleaving '10-23' DNAzymes with enhanced stability and activity

‘10-23’ DNAzymes can be used to cleave any target RNA in a sequence-specific manner. For applications in vivo, they have to be stabilised against nucleolytic attack by the introduction of modified nucleotides without obstructing cleavage activity. In this study, we optimise the design of a DNAzyme targeting the 5′-non-translated region of the human rhinovirus 14, a common cold virus, with regard to its kinetic properties and its stability against nucleases. We compare a large number of DNAzymes against the same target site that are stabilised by the use of a 3′-3′-inverted thymidine, phosphorothioate linkages, 2′-O-methyl RNA and locked nucleic acids, respectively. Both cleavage activity and nuclease stability were significantly enhanced by optimisation of arm length and content of modified nucleotides. Furthermore, we introduced modified nucleotides into the catalytic core to enhance stability against endonucleolytic degradation without abolishing catalytic activity. Our findings enabled us to establish a design for DNAzymes containing nucleotide modifications both in the binding arms and in the catalytic core, yielding a species with up to 10-fold enhanced activity and significantly elevated stability against nucleolytic cleavage. When transferring the design to a DNAzyme against a different target, only a slight modification was necessary to retain activity.     

First song descriptions of some Anatolian species of Tettigoniidae Krauss, 1902 (Orthoptera,Ensifera)

Fourteen endemic and two sub-endemic species belonging to three subfamilies of Tettigoniidae (Tettigoniinae, Bradyporinae and Saginae) were sampled during field trips throughout the different ranges of Anatolia between the years of 2004 and 2013. Acoustic parameters of these 16 species affiliated to 8 genera (Anterastes, Apholidoptera, Gampsocleis, Parapholidoptera, Pezodrymadusa, Psorodonotus, Bradyporus and Saga) have been described for the first time in this study. Acoustical analysis showed that song characters are species-specific in the genera Saga and Psorodonotus. On the other hand, we could not find big differences among species of the genus Pezodrymadusa and Parapholidoptera castaneoviridis species-group.     

Fuzziness and noise in nucleosomal architecture

Nucleosome organization plays a key role in the regulation of gene expression. However, despite the striking advances in the accuracy of nucleosome maps, there are still severe discrepancies on individual nucleosome positioning and how this influences gene regulation. The variability among nucleosome maps, which precludes the fine analysis of nucleosome positioning, might emerge from diverse sources. We have carefully inspected the extrinsic factors that may induce diversity by the comparison of microccocal nuclease (MNase)-Seq derived nucleosome maps generated under distinct conditions. Furthermore, we have also explored the variation originated from intrinsic nucleosome dynamics by generating additional maps derived from cell cycle synchronized and asynchronous yeast cultures. Taken together, our study has enabled us to measure the effect of noise in nucleosome occupancy and positioning and provides insights into the underlying determinants. Furthermore, we present a systematic approach that may guide the standardization of MNase-Seq experiments in order to generate reproducible genome-wide nucleosome patterns.