HotPoint: hot spot prediction server for protein interfaces

The energy distribution along the protein–protein interface is not homogenous; certain residues contribute more to the binding free energy, called ‘hot spots’. Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model. The empirical model incorporates a few simple rules consisting of occlusion from solvent and total knowledge-based pair potentials of residues. The prediction model is computationally efficient and achieves high accuracy of 70%. The input to the HotPoint server is a protein complex and two chain identifiers that form an interface. The server provides the hot spot prediction results, a table of residue properties and an interactive 3D visualization of the complex with hot spots highlighted. Results are also downloadable as text files. This web server can be used for analysis of any protein–protein interface which can be utilized by researchers working on binding sites characterization and rational design of small molecules for protein interactions. HotPoint is accessible at http://prism.ccbb.ku.edu.tr/hotpoint

Effect of Pretreatment on the Enhancement of Biodegradation of Olive Mill Effluent for Treatment in an Anaerobic Cross-Flow Filter Reactor

In this study, various chemical and advanced oxidation processes were tested for enhancement of anaerobic biodegradation of olive mill effluent (OME). The experiments were carried out in a 20 L lab-scale ACF reactor packed with cross-flow filter material made of water-resistant cardboard with a specific surface area of ~300 m2 m–3. The ACF reactor was operated at chosen OLR conditions and fed with different pre-treated OME samples for 240 days (717 days in total). All pretreatment options used in this study improved the anaerobic biological degradation in terms of COD, phenolics and color removal efficiencies. Best effluent quality (5700±250 mg COD per liter) was obtained by using the Fenton process as a pre-treatment. This effluent value is still higher than the official discharge limit for COD (4000 mg COD per liter) in Turkey. Therefore, additional final treatment (e.g. membrane filtration) may be required before discharging into the sewer line

Effects of Cultural Practices on Total Phenolics and Vitamin C Content of Organic Table Grapes

The total phenolic and vitamin C contents of organic table grapes were determined by spectrophotometry and HPLC, respectively, after several quality-increasing treatments were applied at véraison for two growing seasons. Cane girdling and cluster-berry thinning resulted in different responses in the cultivars. ‘Red Globe’ generally was found to produce the lowest quantity of total phenolics in the berries, while ‘Trakya Ilkeren’ was the cultivar that accumulated the highest phenolics. Vitamin C accumulation in the berries was also affected by the treatments. The effect of the treatments was inconclusive in ‘Buca Razakısı’. The application of both girdling and thinning caused more accumulation of vitamin C in the ‘Alphonse L.’ and ‘Trakya Ilkeren’ berries

Reentrant Phase Transitions of the Blume-Emery-Griffiths Model for a Simple Cubic Lattice on the Cellular Automaton

The spin-1 Ising (BEG) model with the nearest-neighbour bilinear and biquadratic interactions and single-ion anisotropy is simulated on a cellular automaton which improved from the Creutz cellular automaton(CCA) for a simple cubic lattice. The simulations have been made for several sets of parameters $K/J$ and $D/J$ in the $-3<D/J\leq 0$ and $-1\leq K/J\leq 0$ parameter regions. The re-entrant and double re-entrant phase transitions of the BEG model are determined from the temperature variations of the thermodynamic quantities ($M$, $Q$ and $\chi$). The phase diagrams characterizing phase transitions are compared with those obtained from other methods.Comment: 12 pages 7 figure

HotSprint: database of computational hot spots in protein interfaces

We present a new database of computational hot spots in protein interfaces: HotSprint. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006. The conserved residues in interfaces with certain buried accessible solvent area (ASA) and complex ASA thresholds are flagged as computational hot spots. The predicted hot spots are observed to correlate with the experimental hot spots with an accuracy of 76%. Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others. A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces. HotSprint is available at http://prism.ccbb.ku.edu.tr/hotsprint; and it provides information for interface residues that are functionally and structurally important as well as the evolutionary history and solvent accessibility of residues in interfaces

A Jupiter-mass planet around the K0 giant HD 208897

For over 10 years, we have carried out a precise radial velocity (RV) survey to find substellar companions around evolved G,K-type stars to extend our knowledge of planet formation and evolution. We performed high precision RV measurements for the giant star HD 208897 using an iodine (I2) absorption cell. The measurements were made at T\"UB\.ITAK National Observatory (TUG, RTT150) and Okayama Astrophysical Observatory (OAO). For the origin of the periodic variation seen in the RV data of the star, we adopted a Keplerian motion caused by an unseen companion. We found that the star hosts a planet with a minimum mass of m2sini=1.40MJ, which is relatively low compared to those of known planets orbiting evolved intermediate-mass stars. The planet is in a nearly circular orbit with a period of P=353 days at about 1 AU distance from the host star. The star is metal rich and located at the early phase of ascent along the red giant branch. The photometric observations of the star at Ankara University Kreiken Observatory (AUKR) and the HIPPARCOS photometry show no sign of variation with periods associated with the RV variation. Neither bisector velocity analysis nor analysis of the Ca II and Halpha lines shows any correlation with the RV measurements

Cytogenetic analysis on Turkonalassus quercanus Keskin, Nabozhenko et Alpagut-Keskin, 2017 (Coleoptera: Tenebrionidae: Helopini)

Cytogenetic features of the endemic Western Anatolian tenebrionid species Turkonalassus quercanus Keskin, Nabozhenko et Alpagut-Keskin, 2017 were analyzed using conventional and differential staining. Chromosome preparations were obtained from the gonads of both males and females. The karyotype of T. quercanus was found to be 2n = 20 (9 + Xyp), which is considered the modal number for Tenebrionidae. The heteromorphic sex chromosomes of T. quercanus form a parachute like bivalent at metaphase I (MI) of male meiosis. Both conventional and differential staining have shown that predominantly metacentric chromosomes of T. quercanus exhibit a typical pericentromeric heterochromatin pattern. As per results of the silver staining, the existence of a prominent nucleolus at prophase I and a highly impregnated area associated with Xyp at MI are indicated the sex chromosomal location of NOR. In comparison with previously published cytogenetic data on other species of the tribe Helopini which are presenting the same karyotype formula, our results suggest that a series of chromosomal rearrangements may have been involved in their karyotype evolution

Extracción asistida por microondas de compuestos no polares de cáscaras de pistacho y caracterización de los extractos

Soxhlet and microwave assisted extraction (MAE) methods were used to obtain non-polar compounds from pistachio hull. MAE parameters (liquid to solid ratio, microwave power, and extraction time) were studied to obtain maximum extraction yield. The optimal conditions were found to be liquid to solid ratio of 15:1 (v/w), microwave power of 250 W and extraction time of 12.5 min. The extraction yields were 9.81 and 9.50% for MAE and Soxhlet methods, respectively. The total phenolic content, antioxidant activity and tocopherol content of the extract obtained by MAE was found to be significantly higher than those of the Soxhlet extract (p < 0.05). The results showed that the extract contained α-tocopherols (567.65 mg/kg) and oleic acid (48.46%) as the major tocopherols and fatty acids. These findings propose that hull extracts can be considered as a good source of natural bioactive compounds and MAE can be a good alternative to the traditional Soxhlet method.Se utilizó la extracción mediante Soxhlet y métodos de extracción asistida mediante microondas (MAE) para obtener compuestos no polares de las cascaras de pistacho. Se estudiaron los parámetros para la MAE (relación líquido-sólido, potencia de microondas y tiempo de extracción) para obtener el máximo rendimiento de la extracción. Se encontró que las condiciones óptimas eran una relación líquido a sólido de 15:1 (v/p), potencia de microondas de 250 W y un tiempo de extracción de 12,5 minutos. Los rendimientos de extracción fueron 9.81 y 9.50% para los métodos MAE y Soxhlet, respectivamente. El contenido fenólico total, la actividad antioxidante y el contenido de tocoferoles de los extractos obtenidos por MAE fueron significativamente más altos que los de los extractos de Soxhlet (p < 0,05). Los resultados muestran que el extracto contiene α-tocoferol (567.65 mg/kg) y ácido oleico (48.46%) como los principales tocoferoles y ácidos grasos, respectivamente. Estos hallazgos proponen que los extractos de las cascaras pueden considerarse como una buena fuente de compuestos bioactivos naturales y MAE puede ser una buena alternativa al método Soxhlet tradicional

What tweets tell us about MOOC participation

In this research paper, the authors analyze the collected Twitter data output during MobiMOOC 2011. This six-week data stream includes all tweets that contain the MOOC's hashtag (#mobiMOOC) and it has been analyzed using qualitative methodology. The analysis sought to examine the emotive vocabulary used, to determine if there was content-sharing via tweets, and to analyze the folksonomic trends of the tweets. In Addition sought a deeper understanding of what, and how, MOOC participants share what they share on the MOOC's Twitter channel. The aim of this study is to provide a little more insight into MOOC learner behaviors on Twitter so that future MOOC designers and facilitators can better engage with their learners.Facultad de Ciencias Exacta