Characterization of CoRoT target fields with BEST: Identification of periodic variable stars in the IR01 field

We report on observations of the CoRoT IR01 field with the Berlin Exoplanet Search Telescope (BEST). BEST is a small aperture telescope with a wide field of view (FOV). It is dedicated to search for variable stars within the target fields of the CoRoT space mission to aid in minimizing false-alarm rates and identify potential targets for additional science. CoRoT's observational programm started in February 2007 with the "initial run" field (IR01) observed for about two months. BEST observed this field for 12 nights spread over three months in winter 2006. From the total of 30426 stars observed in the IR01 field 3769 were marked as suspected variable stars and 54 from them showed clear periodicity. From these 19 periodic stars are within the part of the CoRoT FOV covered in our data set

Biomarker Response to Galactic Cosmic Ray-Induced NOx and the Methane Greenhouse Effect in the Atmosphere of an Earthlike Planet Orbiting an M-Dwarf Star

Planets orbiting in the habitable zone (HZ) of M-Dwarf stars are subject to high levels of galactic cosmic rays (GCRs) which produce nitrogen oxides in earthlike atmospheres. We investigate to what extent this NOx may modify biomarker compounds such as ozone (O3) and nitrous oxide (N2O), as well as related compounds such as water (H2O) (essential for life) and methane (CH4) (which has both abiotic and biotic sources) . Our model results suggest that such signals are robust, changing in the M-star world atmospheric column by up to 20% due to the GCR NOx effects compared to an M-star run without GCR effects and can therefore survive at least the effects of galactic cosmic rays. We have not however investigated stellar cosmic rays here. CH4 levels are about 10 times higher than on the Earth related to a lowering in hydroxyl (OH) in response to changes in UV. The increase is less than reported in previous studies. This difference arose partly because we used different biogenic input. For example, we employed 23% lower CH4 fluxes compared to those studies. Unlike on the Earth, relatively modest changes in these fluxes can lead to larger changes in the concentrations of biomarker and related species on the M-star world. We calculate a CH4 greenhouse heating effect of up to 4K. O3 photochemistry in terms of the smog mechanism and the catalytic loss cycles on the M-star world differs considerably compared with the Earth

CRAF R391W is a melanoma driver oncogene.

Approximately 75% of melanomas have known driver oncogenic mutations in BRAF, NRAS, GNA11 or GNAQ, while the mutations providing constitutive oncogenic signaling in the remaining melanomas are not known. We established a melanoma cell line from a tumor with none of the common driver mutations. This cell line demonstrated a signaling profile similar to BRAF-mutants, but lacked sensitivity to the BRAF inhibitor vemurafenib. RNA-seq mutation data implicated CRAF R391W as the alternative driver mutation of this melanoma. CRAF R391W was homozygous and over expressed. These melanoma cells were highly sensitive to CRAF, but not BRAF knockdown. In reconstitution experiments, CRAF R391W, but not CRAF WT, transformed NIH3T3 cells in soft-agar colony formation assays, increased kinase activity in vitro, induced MAP kinase signaling and conferred vemurafenib resistance. MAP kinase inducing activity was dependent on CRAF dimerization. Thus, CRAF is a bona fide alternative oncogene for BRAF/NRAS/GNAQ/GNA11 wild type melanomas

The Berlin Exoplanet Search Telescope II. Catalog of Variable Stars. I. Characterization of Three Southern Target Fields

A photometric survey of three Southern target fields with BEST II yielded the detection of 2,406 previously unknown variable stars and an additional 617 stars with suspected variability. This study presents a catalog including their coordinates, magnitudes, light curves, ephemerides, amplitudes, and type of variability. In addition, the variability of 17 known objects is confirmed, thus validating the results. The catalog contains a number of known and new variables that are of interest for further astrophysical investigations, in order to, e.g., search for additional bodies in eclipsing binary systems, or to test stellar interior models. Altogether, 209,070 stars were monitored with BEST II during a total of 128 nights in 2009/2010. The overall variability fraction of 1.2-1.5% in these target fields is well comparable to similar ground-based photometric surveys. Within the main magnitude range of $R\in\left[11,17\right]$, we identify 0.67(3)% of all stars to be eclipsing binaries, which indicates a completeness of about one third for this particular type in comparison to space surveys.Comment: accepted to A

Variability survey in the CoRoT SRa01 field: Implications of eclipsing binary distribution on cluster formation in NGC 2264

Time-series photometry of the CoRoT field SRa01 was carried out with the Berlin Exoplanet Search Telescope II (BEST II) in 2008/2009. A total of 1,161 variable stars were detected, of which 241 were previously known and 920 are newly found. Several new, variable young stellar objects have been discovered. The study of the spatial distribution of eclipsing binaries revealed the higher relative frequency of Algols toward the center of the young open cluster NGC 2264. In general Algol frequency obeys an isotropic distribution of their angular momentum vectors, except inside the cluster, where a specific orientation of the inclinations is the case. We suggest that we see the orbital plane of the binaries almost edge-on.Comment: 18 pages, 8 figures, accepted for publication in Ap

JUN dependency in distinct early and late BRAF inhibition adaptation states of melanoma.

A prominent mechanism of acquired resistance to BRAF inhibitors in BRAF (V600) -mutant melanoma is associated with the upregulation of receptor tyrosine kinases. Evidences suggested that this resistance mechanism is part of a more complex cellular adaptation process. Using an integrative strategy, we found this mechanism to invoke extensive transcriptomic, (phospho-) proteomic and phenotypic alterations that accompany a cellular transition to a de-differentiated, mesenchymal and invasive state. Even short-term BRAF-inhibitor exposure leads to an early adaptive, differentiation state change-characterized by a slow-cycling, persistent state. The early persistent state is distinct from the late proliferative, resistant state. However, both differentiation states share common signaling alterations including JUN upregulation. Motivated by the similarities, we found that co-targeting of BRAF and JUN is synergistic in killing fully resistant cells; and when used up-front, co-targeting substantially impairs the formation of the persistent subpopulation. We confirmed that JUN upregulation is a common response to BRAF inhibitor treatment in clinically treated patient tumors. Our findings demonstrate that events shared between early- and late-adaptation states provide candidate up-front co-treatment targets

Periodic variable stars in CoRoT field LRa02 observed with BEST II

The Berlin Exoplanet Search Telescope II (BEST II) is a small wide field-of-view photometric survey telescope system located at the Observatorio Cerro Armazones, Chile. The high duty cycle combined with excellent observing conditions and millimagnitude photometric precision makes this instrument suitable for ground based support observations for the CoRoT space mission. Photometric data of the CoRoT LRa02 target field collected between November 2008 and March 2009 were analysed for stellar variability. The presented results will help in the future analysis of the CoRoT data, particularly in additional science programs related to variable stars. BEST II observes selected CoRoT target fields ahead of the space mission. The photometric data acquired are searched for stellar variability, periodic variable stars are identified with time series analysis of the obtained stellar light curves. We obtained the light curves of 104335 stars in the CoRoT LRa02 field over 41 nights. Variability was detected in light curves of 3726 stars of which 350 showed a regular period. These stars are, with the exception of 5 previously known variable stars, new discoveries.Comment: The figures with light curves can be find in the A&A journal as online onl

Fitting a geometric graph to a protein-protein interaction network

Finding a good network null model for protein-protein interaction (PPI) networks is a fundamental issue. Such a model would provide insights into the interplay between network structure and biological function as well as into evolution. Also, network (graph) models are used to guide biological experiments and discover new biological features. It has been proposed that geometric random graphs are a good model for PPI networks. In a geometric random graph, nodes correspond to uniformly randomly distributed points in a metric space and edges (links) exist between pairs of nodes for which the corresponding points in the metric space are close enough according to some distance norm. Computational experiments have revealed close matches between key topological properties of PPI networks and geometric random graph models. In this work, we push the comparison further by exploiting the fact that the geometric property can be tested for directly. To this end, we develop an algorithm that takes PPI interaction data and embeds proteins into a low-dimensional Euclidean space, under the premise that connectivity information corresponds to Euclidean proximity, as in geometric-random graphs.We judge the sensitivity and specificity of the fit by computing the area under the Receiver Operator Characteristic (ROC) curve. The network embedding algorithm is based on multi-dimensional scaling, with the square root of the path length in a network playing the role of the Euclidean distance in the Euclidean space. The algorithm exploits sparsity for computational efficiency, and requires only a few sparse matrix multiplications, giving a complexity of O(N2) where N is the number of proteins.The algorithm has been verified in the sense that it successfully rediscovers the geometric structure in artificially constructed geometric networks, even when noise is added by re-wiring some links. Applying the algorithm to 19 publicly available PPI networks of various organisms indicated that: (a) geometric effects are present and (b) two-dimensional Euclidean space is generally as effective as higher dimensional Euclidean space for explaining the connectivity. Testing on a high-confidence yeast data set produced a very strong indication of geometric structure (area under the ROC curve of 0.89), with this network being essentially indistinguishable from a noisy geometric network. Overall, the results add support to the hypothesis that PPI networks have a geometric structure