Virtual Research Environments for Environmental and Earth Sciences: Approaches and Experiences

Virtual Research Environments (VREs) are playing an increasingly important role in data centric sciences. Also, the concept is known as Science Gateways in North America where generally the functionality is portal plus workflow deployment and Virtual Laboratories in Australia where the end-user can compose a complete system from the user interface to use of e-Infrastructures by a 'pick and mix' process from the offered assets. The key aspect is to provide an environment wherein the end-user - researcher, policymaker, commercial enterprise or citizen scientist - has available with an integrating interface all the assets needed to achieve their objectives. These aspects are explored through different approaches related to ENVRI

Trialkylammonium salt degradation: implications for methylation and cross-coupling

Trialkylammonium (most notably N,N,N-trimethylanilinium) salts are known to display dual reactivity through both the aryl group and the N-methyl groups. These salts have thus been widely applied in cross-coupling, aryl etherification, fluorine radiolabelling, phase-transfer catalysis, supramolecular recognition, polymer design, and (more recently) methylation. However, their application as electrophilic methylating reagents remains somewhat underexplored, and an understanding of their arylation versus methylation reactivities is lacking. This study presents a mechanistic degradation analysis of N,N,N-trimethylanilinium salts and highlights the implications for synthetic applications of this important class of salts. Kinetic degradation studies, in both solid and solution phases, have delivered insights into the physical and chemical parameters affecting anilinium salt stability. 1H NMR kinetic analysis of salt degradation has evidenced thermal degradation to methyl iodide and the parent aniline, consistent with a closed-shell SN2-centred degradative pathway, and methyl iodide being the key reactive species in applied methylation procedures. Furthermore, the effect of halide and non-nucleophilic counterions on salt degradation has been investigated, along with deuterium isotope and solvent effects. New mechanistic insights have enabled the investigation of the use of trimethylanilinium salts in O-methylation and in improved cross-coupling strategies. Finally, detailed computational studies have helped highlight limitations in the current state-of-the-art of solvation modelling of reaction in which the bulk medium undergoes experimentally observable changes over the reaction timecourse

Antimicrobial activity of some Sri Lankan Rubiaceae and Meliaceae

Ninety solvent extracts (n-hexane, dichloromethane and methanol) obtained from the leaves, bark and stem of 13 Sri Lankan Rubiaceae and two Sri Lankan Meliaceae plants have been screened for antibacterial and antifungal activities. Morinda tinctoria, Mussaenda frondosa, Psychotria gardneri and Psychotria stenophylla displayed the widest spectrum of antibacterial activity

Indications to hospital admission and isolation of children with possible or defined tuberculosis : Systematic review and proposed recommendations for pediatric patients leaving in developed countries

Tuberculosis (TB) is a re-emerging health problem in developed countries. This paper is part of large guidelines on the global management of TB in children, by a group of scientific societies. It describes the indications to hospitalization of children with suspected or diagnosed TB, the isolation measures, hospital discharge, and re-admission into the community. Using the Consensus Conference method, relevant publications in English were identified by means of a systematic review of MEDLINE and the Cochrane Database of Systematic Reviews from their inception until 31 December 2014. Available data on indications to hospitalization were mainly indirect and largely derived from observational studies. They include: (1) host-related risk factors, the main being age <12 months, immune deficiencies, and malnutrition; (2) TB-related clinical conditions that resemble those of pneumonia but also include drug-resistance; and (3) social and logistic conditions. The latter are based on opinion and depend on local conditions. Analysis of the literature showed that patients hospitalized with suspected pulmonary TB should be put in precautionary respiratory isolation regardless of their age while they await diagnosis. The general conditions for re-admission into the community are at least 14 days of effective treatment and negative microscopic tests of 3 consecutive samples in previously microscopically positive patients. This is the first paper that provides indications to hospitalization of children with TB. Most recommendations are generally applicable in all developed countries. Some might need an adaptation to local setting, epidemiological, parameters, and availability of specific health-care facilities

Secondary metabolites of the sponge-derived fungus Acremonium persicinum

This study reports the isolation and characterization of six new acremine metabolites, 5-chloroacremine A (4), 5-chloroacremine H (5), and acremines 0 (6), P (7), Q(8), and R (9), together with the known acremines A (1), F (2), and N (3) from the fungus Acremonium persicinum cultured from the marine sponge Anomoianthella rubra. The relative configuration of acremine F (2) was determined by analyses of proton coupling constant values and NOESY data, and the absolute configuration confirmed as (IS, 4S, 6R) by X-ray crystallographic analysis of the borate ester derivative 15. Acremines O, P, and R were each shown to be of 8R configuration by H-1 NMR analyses of MPA esters. The relative configurations suggested for acremines P and Q were each deduced by molecular modeling together with NOESY and coupling constant data. The (3)J(H-C) values in acremine P were measured using the pulse sequence EXSIDE, and the observed (3)J(H8-C4) of 5.4 Hz and small (3)J(H-C) values

Species concepts in Cercospora: spotting the weeds among the roses

The genus Cercospora contains numerous important plant pathogenic fungi from a diverse range of hosts. Most species of Cercospora are known only from their morphological characters in vivo. Although the genus contains more than 5 000 names, very few cultures and associated DNA sequence data are available. In this study, 360 Cercospora isolates, obtained from 161 host species, 49 host families and 39 countries, were used to compile a molecular phylogeny. Partial sequences were derived from the internal transcribed spacer regions and intervening 5.8S nrRNA, actin, calmodulin, histone H3 and translation elongation factor 1-alpha genes. The resulting phylogenetic clades were evaluated for application of existing species names and five novel species are introduced. Eleven species are epi-, lecto- or neotypified in this study. Although existing species names were available for several clades, it was not always possible to apply North American or European names to African or Asian strains and vice versa. Some species were found to be limited to a specific host genus, whereas others were isolated from a wide host range. No single locus was found to be the ideal DNA barcode gene for the genus, and species identification needs to be based on a combination of gene loci and morphological characters. Additional primers were developed to supplement those previously published for amplification of the loci used in this study. TAXONOMIC NOVELTIES: New species - Cercospora coniogrammes Crous &amp; R.G. Shivas, Cercospora delaireae C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora euphorbiae-sieboldianae C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora pileicola C. Nakash., Crous, U. Braun &amp; H.D. Shin, Cercospora vignigena C. Nakash., Crous, U. Braun &amp; H.D. Shin. Typifications: epitypifications - Cercospora alchemillicola U. Braun &amp; C.F. Hill, Cercospora althaeina Sacc., Cercospora armoraciae Sacc., Cercospora corchori Sawada, Cercospora mercurialis Pass., Cercospora olivascens Sacc., Cercospora violae Sacc.; neotypifications - Cercospora fagopyri N. Nakata &amp; S. Takim., Cercospora sojina Hara

Light regulation of metabolic pathways in fungi

Light represents a major carrier of information in nature. The molecular machineries translating its electromagnetic energy (photons) into the chemical language of cells transmit vital signals for adjustment of virtually every living organism to its habitat. Fungi react to illumination in various ways, and we found that they initiate considerable adaptations in their metabolic pathways upon growth in light or after perception of a light pulse. Alterations in response to light have predominantly been observed in carotenoid metabolism, polysaccharide and carbohydrate metabolism, fatty acid metabolism, nucleotide and nucleoside metabolism, and in regulation of production of secondary metabolites. Transcription of genes is initiated within minutes, abundance and activity of metabolic enzymes are adjusted, and subsequently, levels of metabolites are altered to cope with the harmful effects of light or to prepare for reproduction, which is dependent on light in many cases. This review aims to give an overview on metabolic pathways impacted by light and to illustrate the physiological significance of light for fungi. We provide a basis for assessment whether a given metabolic pathway might be subject to regulation by light and how these properties can be exploited for improvement of biotechnological processes