Upregulated wnt-11 and mir-21 expression trigger epithelial mesenchymal transition in aggressive prostate cancer cells

Prostate cancer (PCa) is the second-leading cause of cancer-related death among men. microRNAs have been identified as having potential roles in tumorigenesis. An oncomir, miR-21, is commonly highly upregulated in many cancers, including PCa, and showed correlation with the Wnt-signaling axis to increase invasion. Wnt-11 is a developmentally regulated gene and has been found to be upregulated in PCa, but its mechanism is unknown. The present study aimed to investigate the roles of miR-21 and Wnt-11 in PCa in vivo and in vitro. First, different Gleason score PCa tissue samples were used; both miR-21 and Wnt-11 expressions correlate with high Gleason scores in PCa patient tissues. This data then was confirmed with formalin-fixed paraffin cell blocks using PCa cell lines LNCaP and PC3. Cell survival and colony formation studies proved that miR-21 involves in cells’ behaviors, as well as the epithelial-mesenchymal transition. Consistent with the previous data, silencing miR-21 led to significant inhibition of cellular invasiveness. Overall, these results suggest that miR-21 plays a significant role related to Wnt-11 in the pathophysiology of PCa

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

HotRegion: a database of predicted hot spot clusters

Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. HotRegion is accessible at http://prism.ccbb.ku.edu.tr/hotregion

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

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

Absolute properties of the binary system BB pegasi

We present ground-based photometry of the low-temperature contact binary BB Peg. We collected all the times of mid-eclipse available in the literature and combined them with those obtained in this study. Analyses of the data indicate a period increase of (3.0 ± 0.1) × 10-8 days yr -1. This period increase of BB Peg can be interpreted in terms of the mass transfer 2.4 × 10-8 M⊙ yr-1 from the less massive to the more massive component. The physical parameters have been determined as Mc = 1.42M⊙, Mh = 0.53 M⊙, Rc = 1.29 R⊙, Rh, = 0.83 R⊙, Lc = 1.86 L⊙, and L h = 0.94 L⊙ through simultaneous solutions of light and of the radial velocity curves. The orbital parameters of the third body, which orbits the contact system in an eccentric orbit, were obtained from the period variation analysis. The system is compared to the similar binaries in the Hertzsprung-Russell and mass-radius diagrams.Ege University Research Fund and TÜBİTAK National Observator

Marginally low mass ratio close binary system V1191 Cyg

In this study, we present photometric and spectroscopic variations of the extremely small mass ratio ($q\simeq 0.1$) late-type contact binary system \astrobj{V1191 Cyg}. The parameters for the hot and cooler companions have been determined as $M_\textrm{h}$ = 0.13 (1) $M_{\odot}$, $M_\textrm{c}$ = 1.29 (8) $M_{\odot}$, $R_\textrm{h}$ = 0.52 (15) $R_{\odot}$, $R_\textrm{c}$ = 1.31 (18) $R_{\odot}$, $L_\textrm{h}$ = 0.46 (25) $L_{\odot}$, $L_\textrm{c}$ = 2.71 (80) $L_{\odot}$, the separation of the components is $a$= 2.20(8) $R_{\odot}$ and the distance of the system is estimated as 278(31) pc. Analyses of the times of minima indicates a period increase of $\frac{dP}{dt}=1.3(1)\times 10^{-6}$ days/yr that reveals a very high mass transfer rate of $\frac{dM}{dt}=2.0(4)\times 10^{-7}$$M_{\odot}$/yr from the less massive component to the more massive one. New observations show that the depths of the minima of the light curve have been interchanged.Comment: Accepted for publication in New Astronomy, 16 pages, 2 figures, 4 table

Astronomical Site Selection for Turkey Using GIS Techniques

A site selection of potential observatory locations in Turkey have been carried out by using Multi-Criteria Decision Analysis (MCDA) coupled with Geographical Information Systems (GIS) and satellite imagery which in turn reduced cost and time and increased the accuracy of the final outcome. The layers of cloud cover, digital elevation model, artificial lights, precipitable water vapor, aerosol optical thickness and wind speed were studied in the GIS system. In conclusion of MCDA, the most suitable regions were found to be located in a strip crossing from southwest to northeast including also a diverted region in southeast of Turkey. These regions are thus our prime candidate locations for future on-site testing. In addition to this major outcome, this study has also been applied to locations of major observatories sites. Since no goal is set for \textit{the best}, the results of this study is limited with a list of positions. Therefore, the list has to be further confirmed with on-site tests. A national funding has been awarded to produce a prototype of an on-site test unit (to measure both astronomical and meteorological parameters) which might be used in this list of locations.Comment: 17 pages, 10 figures, accepted by Experimental Astronom

Identification of differentially expressed subnetworks based on multivariate ANOVA

<p>Abstract</p> <p>Background</p> <p>Since high-throughput protein-protein interaction (PPI) data has recently become available for humans, there has been a growing interest in combining PPI data with other genome-wide data. In particular, the identification of phenotype-related PPI subnetworks using gene expression data has been of great concern. Successful integration for the identification of significant subnetworks requires the use of a search algorithm with a proper scoring method. Here we propose a multivariate analysis of variance (MANOVA)-based scoring method with a greedy search for identifying differentially expressed PPI subnetworks.</p> <p>Results</p> <p>Given the MANOVA-based scoring method, we performed a greedy search to identify the subnetworks with the maximum scores in the PPI network. Our approach was successfully applied to human microarray datasets. Each identified subnetwork was annotated with the Gene Ontology (GO) term, resulting in the phenotype-related functional pathway or complex. We also compared these results with those of other scoring methods such as <it>t </it>statistic- and mutual information-based scoring methods. The MANOVA-based method produced subnetworks with a larger number of proteins than the other methods. Furthermore, the subnetworks identified by the MANOVA-based method tended to consist of highly correlated proteins.</p> <p>Conclusion</p> <p>This article proposes a MANOVA-based scoring method to combine PPI data with expression data using a greedy search. This method is recommended for the highly sensitive detection of large subnetworks.</p