The representation of the West-African Monsoon vertical cloud structure in the Met Office Unified Model: an evaluation with CloudSat

Weather and climate model simulations of the West African Monsoon (WAM) have generally poor representation of the rainfall distribution and monsoon circulation because key processes, such as clouds and convection, are poorly characterized. The vertical distribution of cloud and precipitation during the WAM are evaluated in Met Office Unified Model simulations against CloudSat observations. Simulations were run at 40-km and 12-km horizontal grid length using a convection parameterization scheme and at 12-km, 4-km, and 1.5-km grid length with the convection scheme effectively switched off, to study the impact of model resolution and convection parameterization scheme on the organisation of tropical convection. Radar reflectivity is forward-modelled from the model cloud fields using the CloudSat simulator to present a like-with-like comparison with the CloudSat radar observations. The representation of cloud and precipitation at 12-km horizontal grid length improves dramatically when the convection parameterization is switched off, primarily because of a reduction in daytime (moist) convection. Further improvement is obtained when reducing model grid length to 4 km or 1.5 km, especially in the representation of thin anvil and mid-level cloud, but three issues remain in all model configurations. Firstly, all simulations underestimate the fraction of anvils with cloud top height above 12 km, which can be attributed to too low ice water contents in the model compared to satellite retrievals. Secondly, the model consistently detrains mid-level cloud too close to the freezing level, compared to higher altitudes in CloudSat observations. Finally, there is too much low-level cloud cover in all simulations and this bias was not improved when adjusting the rainfall parameters in the microphysics scheme. To improve model simulations of the WAM, more detailed and in-situ observations of the dynamics and microphysics targeting these non-precipitating cloud types are required.

Nicked-site substrates for a serine recombinase reveal enzyme–DNA communications and an essential tethering role of covalent enzyme–DNA linkages

To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase Tn3 resolvase, we made modified recombination sites with a single-strand nick in one of the two DNA strands. Resolvase acting on these sites cleaves the intact strand very rapidly, giving an abnormal half-site product which accumulates. We propose that these reactions mimic second-strand cleavage of an unmodified site. Cleavage occurs in a synapse of two sites, held together by a resolvase tetramer; cleavage at one site stimulates cleavage at the partner site. After cleavage of a nicked-site substrate, the half-site that is not covalently linked to a resolvase subunit dissociates rapidly from the synapse, destabilizing the entire complex. The covalent resolvase–DNA linkages in the natural reaction intermediate thus perform an essential DNA-tethering function. Chemical modifications of a nicked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibition of resolvase-mediated cleavage and effects on resolvase binding and synapsis, providing insight into the serine recombinase catalytic mechanism and how resolvase interacts with the substrate DNA.

Design of a unified data with business rules storage model for OLTP and OLAP systems

This paper reviews the literature concerning the practice of using Online Analytical Processing (OLAP) systems to recall information stored by Online Transactional Processing (OLTP) systems. Such a review provides a basis for discussion on the need for the information that are recalled through OLAP systems to maintain the contexts of transactions with the data captured by the respective OLTP system. The paper observes an industry trend involving the use of OLTP systems to process information into data, which are then stored in databases without the business rules that were used to process information and data stored in OLTP databases without associated business rules. This includes the necessitation of a practice, whereby, sets of business rules are used to extract, cleanse, transform and load data from disparate OLTP systems into OLAP databases to support the requirements for complex reporting and analytics. These sets of business rules are usually not the same as business rules used to capture data in particular OLTP systems. The paper argues that, differences between the business rules used to interpret these same data sets, risk gaps in semantics between information captured by OLTP systems and information recalled through OLAP systems. Literature concerning the modeling of business transaction information as facts with context as part of the modelling of information systems were reviewed to identify design trends that are contributing to the design quality of OLTP and OLAP systems. The paper then argues that; the quality of OLTP and OLAP systems design has a critical dependency on the capture of facts with associated context, encoding facts with contexts into data with business rules, storage and sourcing of data with business rules, decoding data with business rules into the facts with the context and recall of facts with associated contexts. The paper proposes UBIRQ, a design model to aid the co-design of data with business rules storage for OLTP and OLAP purposes. The proposed design model provides the opportunity for the implementation and use of multi-purpose databases, and business rules stores for OLTP and OLAP systems. Such implementations would enable the use of OLTP systems to record and store data with executions of business rules, which will allow for the use of OLTP and OLAP systems to query data with business rules used to capture the data. Thereby ensuring information recalled via OLAP systems preserves the contexts of transactions as per the data captured by the respective OLTP system.

Towards a unified approach for the determination of the bioaccessibility of organic pollutants

Bioaccessibility studies have been widely used as a research tool to determine the potential human exposure to ingested contaminants. More recently they have been practically applied for soil borne toxic elements. This paper reviews the application of bioaccessibility tests across a range of organic pollutants and contaminated matrices. Important factors are reported to be: the physiological relevance of the test, the components in the gut media, the size fraction chosen for the test and whether it contains a sorptive sink. The bioaccessibility is also a function of the composition of the matrix (e.g. organic carbon content of soils) and the physico-chemical characteristics of the pollutant under test. Despite the widespread use of these tests, there are a large number of formats used and very few validation studies with animal models. We propose a unified format for a bioaccessibility test for organic pollutants. The robustness of this test should first be confirmed through inter laboratory comparison, then tested in-vivo.

Proposal for a unified nomenclature for target site mutations associated with resistance to fungicides

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino-acid substitutions is to cite the wild type amino acid, the codon number and the new amino acid, using the one letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the current paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well-studied “archetype” species. Orthologous amino acids in all species are then assigned numerical “labels” based on the position of the amino acid in the archetype protein.

Evaluation of the Plant–Craig stochastic convection scheme (v2.0) in the ensemble forecasting system MOGREPS-R (24 km) based on the Unified Model (v7.3)

The Plant–Craig stochastic convection parameterization (version 2.0) is implemented in the Met Office Regional Ensemble Prediction System (MOGREPS-R) and is assessed in comparison with the standard convection scheme with a simple stochastic scheme only, from random parameter variation. A set of 34 ensemble forecasts, each with 24 members, is considered, over the month of July 2009. Deterministic and probabilistic measures of the precipitation forecasts are assessed. The Plant–Craig parameterization is found to improve probabilistic forecast measures, particularly the results for lower precipitation thresholds. The impact on deterministic forecasts at the grid scale is neutral, although the Plant–Craig scheme does deliver improvements when forecasts are made over larger areas. The improvements found are greater in conditions of relatively weak synoptic forcing, for which convective precipitation is likely to be less predictable.