In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p ≤ 0.001). Based on this threshold, we identified ∼2,400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches

Doppler tomography of transiting exoplanets: A prograde, low-inclined orbit for the hot Jupiter CoRoT-11b

We report the detection of the Doppler shadow of the transiting hot Jupiter CoRoT-11b. Our analysis is based on line-profile tomography of time-series, Keck/HIRES high-resolution spectra acquired during the transit of the planet. We measured a sky-projected, spin-orbit angle of 0.1 +/- 2.6 degrees, which is consistent with a very low-inclined orbit with respect to the stellar rotation axis. We refined the physical parameters of the system using a Markov chain Monte Carlo simultaneous fitting of the available photometric and spectroscopic data. An analysis of the tidal evolution of the system shows how the currently measured obliquity and its uncertainty translate into an initial absolute value of less than about 10 degrees on the zero-age main sequence, for an expected average modified tidal quality factor of the star Q'* > 4 x 10^6. This is indicative of an inward migration scenario that would not have perturbed the primordial low obliquity of CoRoT-11b. Taking into account the effective temperature and mass of the planet host star (Teff=6440 K, M*=1.23 MSun), the system can be considered a new telling exception to the recently proposed trend, according to which relatively hot and massive stars (Teff>6250 K, M*>1.2 MSun) seem to be preferentially orbited by hot Jupiters with high obliquity.Comment: 5 pages, 4 figures, accepted for publication in A&A Letter

Review of recreational fishing surveys in Western Australia

Recreational fishing has been a popular activity in Western Australia for many years, with an estimated 25% of the population participating in this activity in 2017/18. Recreational fishing surveys have been implemented by the Department of Primary Industries and Regional Development (formally Department of Fisheries) since 1976

Framework for Integration of Data from Remotely Operated Cameras into Recreational Fishery Assessments in Western Australia

Remotely operated cameras can be used for cost-efficient monitoring of recreational fishing activities. This report provides an overview of the current usage of cameras in recreational fishery assessments by the Department of Primary Industries and Regional Development. Since 2006, 32 remotely operated cameras have been installed at 26 locations throughout Western Australia and currently 28 cameras are in use

The spin-orbit angles of the transiting exoplanets WASP-1b, WASP-24b, WASP-38b and HAT-P-8b from Rossiter-McLaughlin observations

We present observations of the Rossiter-McLaughlin effect for the transiting exoplanet systems WASP-1, WASP-24, WASP-38 and HAT-P-8, and deduce the orientations of the planetary orbits with respect to the host stars' rotation axes. The planets WASP-24b, WASP-38b and HAT-P-8b appear to move in prograde orbits and be well aligned, having sky-projected spin orbit angles consistent with zero: {\lambda} = -4.7 \pm 4.0{\deg}, {\lambda} = 15 + 33{\deg}/-43{\deg} and {\lambda} = -9.7 +9.0{\deg}/-7.7{\deg}, respectively. The host stars have Teff < 6250 K and conform with the trend of cooler stars having low obliquities. WASP-38b is a massive planet on a moderately long period, eccentric orbit so may be expected to have a misaligned orbit given the high obliquities measured in similar systems. However, we find no evidence for a large spin-orbit angle. By contrast, WASP-1b joins the growing number of misaligned systems and has an almost polar orbit, {\lambda} = -79 +4.5{\deg}/-4.3{\deg}. It is neither very massive, eccentric nor orbiting a hot host star, and therefore does not share the properties of many other misaligned systems.Comment: Submitted to MNRAS, 13 pages, 8 tables, 6 figures. Includes revised parameter values for WASP-38 and HAT-P-

Magnetically Driven Warping, Precession and Resonances in Accretion Disks

The inner region of the accretion disk onto a rotating magnetized central star (neutron star, white dwarf or T Tauri star) is subjected to magnetic torques which induce warping and precession of the disk. The origin of these torques lies in the interaction between the (induced) surface current on the disk and the horizontal magnetic field (parallel to the disk) produced by the inclined magnetic dipole. Under quite general conditions, there exists a magnetic warping instability in which the magnetic torque drives the disk plane away from the equatorial plane of the star toward a state where the disk normal vector is perpendicular to the spin axis. Viscous stress tends to suppress the warping instability at large radii, but the magnetic torque always dominates as the disk approaches the magnetosphere boundary. The magnetic torque also drives the tilted inner disk into retrograde precession around the stellar spin axis. Moreover, resonant magnetic forcing on the disk can occur which may affect the dynamics of the disk. The magnetically driven warping instability and precession may be related to a number observational puzzles, including: (1) Spin evolution (torque reversal) of accreting X-ray pulsars; (2) Quasi-periodic oscillations in low-mass X-ray binaries; (3) Super-orbital periods in X-ray binaries; (4) Photometric period variations of T Tauri stars.Comment: 39 pages including 1 ps figure; Published version; ApJ, 524, 1030-1047 (1999

Regulation of polarized morphogenesis by protein kinase C iota in oncogenic epithelial spheroids.

Protein kinase C iota (PKCι), a serine/threonine kinase required for cell polarity, proliferation and migration, is commonly up- or downregulated in cancer. PKCι is a human oncogene but whether this is related to its role in cell polarity and what repertoire of oncogenes acts in concert with PKCι is not known. We developed a panel of candidate oncogene expressing Madin-Darby canine kidney (MDCK) cells and demonstrated that H-Ras, ErbB2 and phosphatidylinositol 3-kinase transformation led to non-polar spheroid morphogenesis (dysplasia), whereas MDCK spheroids expressing c-Raf or v-Src were largely polarized. We show that small interfering RNA (siRNA)-targeting PKCι decreased the size of all spheroids tested and partially reversed the aberrant polarity phenotype in H-Ras and ErbB2 spheroids only. This indicates distinct requirements for PKCι and moreover that different thresholds of PKCι activity are required for these phenotypes. By manipulating PKCι function using mutant constructs, siRNA depletion or chemical inhibition, we have demonstrated that PKCι is required for polarization of parental MDCK epithelial cysts in a 3D matrix and that there is a threshold of PKCι activity above and below which, disorganized epithelial morphogenesis results. Furthermore, treatment with a novel PKCι inhibitor, CRT0066854, was able to restore polarized morphogenesis in the dysplastic H-Ras spheroids. These results show that tightly regulated PKCι is required for normal-polarized morphogenesis in mammalian cells and that H-Ras and ErbB2 cooperate with PKCι for loss of polarization and dysplasia. The identification of a PKCι inhibitor that can restore polarized morphogenesis has implications for the treatment of Ras and ErbB2 driven malignancies.Cancer Research UK; Royal Marsden/Institute of Cancer Research National Institute for Health Research Biomedical Research Centre (M.L.)