A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

The complexity ofmany RNA processing pathways is such that a conventional systemsmodelling approach is inadequate to represent all themolecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNApolymerase II (RNAPII)C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 30 end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location atwhich they take place on the genes are a function of the time spent byRNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interactwith theCTD.On this basis,we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics.</p

Water quality, catchment imperviousness and Water Sensitive Urban Design in a small urban stream in Helsinki, Finland

The primary characteristic of urbanisation is the addition of hard surfaces to catchments, which affects water and habitat quality in urban streams and alters natural hydrological processes by reducing infiltration, evapotranpiration and efficiently conveying storm runoff to streams, gathering a variety of urban polluants along the way. This is typical of the 'urban stream syndrome'. Catchment imperviousness (especially Effective Impervious Area or percent connectivity) can be used as one of the primary indicators of the severity of this phenomenon. This research was initiated through a collaboration between the City of Helsinki and the University of Helsinki to determine the baseline water quality of Hakuninmaanoja, a small urban stream in Helsinki, Finland, and the imperviousness of its catchment, where a pilot ecological housing development 'Kuninkaantammi' (KUNTA) will be built beginning in 2013. The purpose of the project is to assess the current characteristics of the catchment prior to the development in the headwaters of the stream. An automatic water quality monitoring station was built on the lower part of the stream approximately 200m upstream of its junction with Mätäjoki, the second largest river of Helsinki. Water Sensitive Urban Design can be used as part of a holistic stormwater treatment train to limit newly created imperviousness, and minimise the connectivity of the necessary remainder, allowing stormwater runoff to be reused, infiltrated and treated through soil media, or slowed down enough to attenuate the urban hydrograph. Some of these features such as raingardens, green roofs and detention ponds will be included in the KUNTA development for this purpose. A detailed calculation of catchment imperviousness was completed via field survey and land use categorization methods. Total Impervious Area (TIA) was determined to be 22%, Effective Impervious Area 15% and catchment wide runoff coefficient given by land use categorisation method to be 0.32. TIA is expected to increase to 30% following development of KUNTA, however EIA is not expected to increase in proportion with TIA due to planned Water Sensitive Urban Design features. Yearly runoff volumes based on each method of calculating imperviousness were estimated, as well as for the future following KUNTA development. Water quality in the stream currently is quite satisfactory in relation to other streams in Helsinki, however the urban stream syndrome is already evident with particular concern regarding temperature, sediment and peak flow fluctuations. Effective Impervious Area should be used in urban planning of new and existing developments rather than TIA because it will give much greater accuracy of runoff volumes and infiltration rates by taking into account unconnected impervious surfaces. Strengthening local solutions to reduce connectivity should be a municipal priority. Water quality monitoring will continue at the site until after KUNTA has been built, and further research should focus on determining the technical performance of stormwater Best Management Practices (BMPs) at the site

How much does education improve intelligence? A meta-analysis

Intelligence test scores and educational duration are positively correlated. This correlation could be interpreted in two ways: Students with greater propensity for intelligence go on to complete more education, or a longer education increases intelligence. We meta-analyzed three categories of quasiexperimental studies of educational effects on intelligence: those estimating education-intelligence associations after controlling for earlier intelligence, those using compulsory schooling policy changes as instrumental variables, and those using regression-discontinuity designs on school-entry age cutoffs. Across 142 effect sizes from 42 data sets involving over 600,000 participants, we found consistent evidence for beneficial effects of education on cognitive abilities of approximately 1 to 5 IQ points for an additional year of education. Moderator analyses indicated that the effects persisted across the life span and were present on all broad categories of cognitive ability studied. Education appears to be the most consistent, robust, and durable method yet to be identified for raising intelligence. </jats:p

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy

High-contrast imager for Complex Aperture Telescopes (HiCAT): 1. Testbed design

Searching for nearby habitable worlds with direct imaging and spectroscopy will require a telescope large enough to provide angular resolution and sensitivity to planets around a significant sample of stars. Segmented telescopes are a compelling option to obtain such large apertures. However, these telescope designs have a complex geometry (central obstruction, support structures, segmentation) that makes high-contrast imaging more challenging. We are developing a new high-contrast imaging testbed at STScI to provide an integrated solution for wavefront control and starlight suppression on complex aperture geometries. We present our approach for the testbed optical design, which defines the surface requirements for each mirror to minimize the amplitude-induced errors from the propagation of out-of-pupil surfaces. Our approach guarantees that the testbed will not be limited by these Fresnel propagation effects, but only by the aperture geometry. This approach involves iterations between classical ray-tracing optical design optimization, and end-to-end Fresnel propagation with wavefront control (e.g. Electric Field Conjugation / Stroke Minimization). The construction of the testbed is planned to start in late Fall 2013.Comment: Proc. of the SPIE 8864, 10 pages, 3 figures, Techniques and Instrumentation for Detection of Exoplanets V

A strong link between speed of visual discrimination and cognitive ageing

SummaryAttempts to explain people’s differences in intelligence and cognitive ageing often hypothesize that they are founded substantially upon differences in speed of information processing [1]. To date, there are no studies that fulfill the design criteria necessary to test this idea, namely: having a large sample size; being sufficiently longitudinal; and using measures of processing efficiency that have a tractable biological basis, are grounded in theory, and are not themselves complex or based on motor response speed. We measured visual ‘inspection time’, a psychophysical indicator of the efficiency of the early stages of perceptual processing [2], in a large (n = 628 with full data), narrow-age sample at mean ages 70, 73, and 76 years. We included concurrent tests of intelligence. A latent growth curve model assessed the extent to which inspection time change is coupled with change in intelligence. Results showed a moderate correlation (r = 0.460) between inspection time performance and intelligence, and a strong correlation between change in inspection time and change in intelligence from 70 to 76 (r = 0.779). These results support the processing speed theory of cognitive ageing. They go beyond cross-sectional correlation to show that cognitive change is accompanied by changes in basic visual information processing as we age

Cnih3 deletion dysregulates dorsal hippocampal transcription across the estrous cycle

In females, the hippocampus, a critical brain region for coordination of learning, memory, and behavior, displays altered physiology and behavioral output across the estrous or menstrual cycle. However, the molecular effectors and cell types underlying these observed cyclic changes have only been partially characterized to date. Recently, profiling of mice null for the AMPA receptor trafficking gen