Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes

Effects of Ionomycin on Egg Activation and Early Development in Starfish

Ionomycin is a Ca2+-selective ionophore that is widely used to increase intracellular Ca2+ levels in cell biology laboratories. It is also occasionally used to activate eggs in the clinics practicing in vitro fertilization. However, neither the precise molecular action of ionomycin nor its secondary effects on the eggs' structure and function is well known. In this communication we have studied the effects of ionomycin on starfish oocytes and zygotes. By use of confocal microscopy, calcium imaging, as well as light and transmission electron microscopy, we have demonstrated that immature oocytes exposed to ionomycin instantly increase intracellular Ca2+ levels and undergo structural changes in the cortex. Surprisingly, when microinjected into the cells, ionomycin produced no Ca2+ increase. The ionomycin-induced Ca2+ rise was followed by fast alteration of the actin cytoskeleton displaying conspicuous depolymerization at the oocyte surface and in microvilli with concomitant polymerization in the cytoplasm. In addition, cortical granules were disrupted or fused with white vesicles few minutes after the addition of ionomycin. These structural changes prevented cortical maturation of the eggs despite the normal progression of nuclear envelope breakdown. At fertilization, the ionomycin-pretreated eggs displayed reduced Ca2+ response, no elevation of the fertilization envelope, and the lack of orderly centripetal translocation of actin fibers. These alterations led to difficulties in cell cleavage in the monospermic zygotes and eventually to a higher rate of abnormal development. In conclusion, ionomycin has various deleterious impacts on egg activation and the subsequent embryonic development in starfish. Although direct comparison is difficult to make between our findings and the use of the ionophore in the in vitro fertilization clinics, our results call for more defining investigations on the issue of a potential risk in artificial egg activation

Shannon information in record data

Record values, Record times, Shannon information, Fisher information, Euler’s constant, Digamma function, Zeta function,

Dynamic water quality modelling and uncertainty analysis of phytoplankton and nutrient cycles for the upper South Saskatchewan River

The surface water quality of the upper South Saskatchewan River was modelled using Water Quality Analysis Simulation Program (WASP) 7.52. Model calibration and validation were based on samples taken from four long-term water quality stations during the period 2007–2009. Parametric sensitivities in winter and summer were examined using root mean square error (RMSE) and relative entropy. The calibration and validation results show good agreement between model prediction and observed data. The two sensitivity methods confirmed pronounced parametric sensitivity to model state variables in summer compared to winter. Of the 24 parameters examined, dissolved oxygen (DO) and ammonia (NH3-N) are the most influenced variables in summer. Instream kinetic processes including nitrification, nutrient uptake by algae and algae respiration induce a higher sensitivity on DO in summer than in winter. Moreover, in summer, soluble reactive phosphorus (SRP) and chlorophyll-a (Chla) variables are more sensitive to algal processes (nutrient uptake and algae death). In winter however, there exists some degree of sensitivity of algal processes (algae respiration and nutrient uptake) to DO and NH3-N. Results of this study provide information on the state of the river water quality which impacts Lake Diefenbaker and the need for additional continuous monitoring in the river. The results of the sensitivity analysis also provide guidance on most sensitive parameters and kinetic processes that affect eutrophication for preliminary surface water quality modelling studies in cold regions