Mapping the potential energy surfaces for ring-closing metathesis reactions of prototypical dienes by electronic structure calculations

The potential energy surfaces for ring-closing metathesis reactions of a series of simple alpha,omega-dienes which lead to 5-10 membered ring products, have been explored using density functional theory methods. We have investigated both the conformational aspects of the hydrocarbon chain during the course of the reactions, as well as the stationary structures on the corresponding potential energy surfaces. Extensive conformational searches reveal that the reaction proceeds via the conformation that would be expected for the cycloalkene product, though most unexpectedly, cyclohexene forms via complexes in boat-like conformations. The M06-L density functional has been used to map out the potential energy surfaces, and has identified metallocyclobutane fragmentation as being generally the highest barrier along the pathway. The structural variations along the pathway have been discussed for the reactant hydrocarbons of differing chain length to identify points at which cyclisation events may begin to affect reaction rates. Our study provides an excellent starting point from which to begin to learn about the way RCM reaction outcomes are controlled by diene structur

A surprising steric effect on a tandem cycloaddition/ring-opening reaction : rapid syntheses of difluorinated analogues of (hydroxymethyl)conduritols

Difluorinated analogues of (hydroxymethyl)conduritols can be synthesised from selected furans and a difluorinated dienophile in two reaction steps

What is the initiation step of the Grubbs-Hoveyda olefin metathesis catalyst?

Density function theory calculations reveal that the Grubbs-Hoveyda olefin metathesis pre-catalyst is activated by the formation of a complex in which the incoming alkene substrate and outgoing alkoxy ligand are both clearly associated with the ruthenium centre. The computed energies for reaction are in good agreement with the experimental values, reported here

Limits of agricultural greenhouse gas calculators to predict soil N2O and CH4 fluxes in tropical agriculture

Acknowledgements This work was undertaken as part of the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), which is a strategic partnership of CGIAR and Future Earth. This research was carried out with funding by the European Union (EU) and with technical support from the International Fund for Agricultural Development (IFAD). The UN FAO Mitigation of Climate Change in Agriculture (MICCA) Programme funded data collection in Kenya and Tanzania. The views expressed in the document cannot be taken to reflect the official opinions of CGIAR, Future Earth, or donors. We thank Louis Bockel of the UN FAO Agricultural Development Economics Division (ESA) for his comments on an earlier draft of the manuscript.Peer reviewedPublisher PD

Modelling CH4 emission from rice ecosystem: A comparison between existing empirical models

Rice is a staple food for more than three billion people and accounts for up to 11% of the global methane (CH4) emissions from anthropogenic sources. With increasing populations, particularly in less developed countries where rice is a major cereal crop, production continues to increase to meet demand. Implementing site-specific mitigation measures to reduce greenhouse gas emissions from rice is important to minimise climate change. Measuring greenhouse gases is costly and time-consuming; therefore, many farmers, supply chains, and scientists rely on greenhouse gas accounting tools or internationally acceptable methodologies (e.g., Intergovernmental Panel on Climate Change) to estimate emissions and explore mitigation options. In this paper, existing empirical models that are widely used have been evaluated against measured CH4 emission data. CH4 emission data and management information were collected from 70 peer-reviewed scientific papers. Model input variables such as soil organic carbon (SOC), pH, water management during crop season and pre-season, and organic amendment application were collected and used for estimation of CH4 emission. The performance of the models was evaluated by comparing the predicted emission values against measured emissions with the result showing that the models capture the impact of different management on emissions, but either under- or overestimate the emission value, and therefore are unable to capture the magnitude of emissions. Estimated emission values are much lower than observed for most of the rice-producing countries, with R correlation coefficient values varying from −0.49 to 0.87 across the models. In conclusion, current models are adequate for predicting emission trends and the directional effects of management, but are not adequate for estimating the magnitude of emissions. The existing models do not consider key site-specific variables such as soil texture, planting method, cultivar type, or growing season, which all influence emissions, and thus, the models lack sensitivity to key site variables to reliably predict emissions

Characteristic QSO Accretion Disk Temperatures from Spectroscopic Continuum Variability

Using Sloan Digital Sky Survey (SDSS) quasar spectra taken at multiple epochs, we find that the composite flux density differences in the rest frame wavelength range 1300-6000 AA can be fit by a standard thermal accretion disk model where the accretion rate has changed from one epoch to the next (without considering additional continuum emission components). The fit to the composite residual has two free parameters: a normalizing constant and the average characteristic temperature $\bar{T}^*$. In turn the characteristic temperature is dependent on the ratio of the mass accretion rate to the square of the black hole mass. We therefore conclude that most of the UV/optical variability may be due to processes involving the disk, and thus that a significant fraction of the UV/optical spectrum may come directly from the disk.Comment: 31 pages, 8 figure

A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans

While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes

Central obesity as a precursor to the metabolic syndrome in the AusDiab study and Mauritius

Evidence from epidemiologic studies that central obesity precedes future metabolic change and does not occur concurrently with the appearance of the blood pressure, glucose, and lipid abnormalities that characterize the metabolic syndrome (MetS) has been lacking. Longitudinal surveys were conducted in Mauritius in 1987, 1992, and 1998, and in Australia in 2000 and 2005 (AusDiab). This analysis included men and women (aged 25 years) in three cohorts: AusDiab 2000&ndash;2005 (n = 5,039), Mauritius 1987&ndash;1992 (n = 2,849), and Mauritius 1987&ndash;1998 (n = 1,999). MetS components included waist circumference, systolic blood pressure, fasting and 2-h postload plasma glucose, high-density lipoprotein (HDL) cholesterol, triglycerides, and homeostasis model assessment of insulin sensitivity (HOMA-S) (representing insulin sensitivity). Linear regression was used to determine which baseline components predicted deterioration in other MetS components over 5 years in AusDiab and 5 and 11 years in Mauritius, adjusted for age, sex, and ethnic group. Baseline waist circumference predicted deterioration (P &lt; 0.01) in four of the other six MetS variables tested in AusDiab, five of six in Mauritius 1987&ndash;1992, and four of six in Mauritius 1987&ndash;1998. In contrast, an increase in waist circumference between baseline and follow-up was only predicted by insulin sensitivity (HOMA-S) at baseline, and only in one of the three cohorts. These results suggest that central obesity plays a central role in the development of the MetS and appears to precede the appearance of the other MetS components.<br /

Prenatal Programming of Metabolic Syndrome in the Common Marmoset Is Associated With Increased Expression of 11β-Hydroxysteroid Dehydrogenase Type 1

OBJECTIVE: Recent studies in humans and animal models of obesity have shown increased adipose tissue activity of 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1), which amplifies local tissue glucocorticoid concentrations. The reasons for this 11beta-HSD1 dysregulation are unknown. Here, we tested whether 11beta-HSD1 expression, like the metabolic syndrome, is "programmed" by prenatal environmental events in a nonhuman primate model, the common marmoset monkey. RESEARCH DESIGN AND METHODS: We used a "fetal programming" paradigm where brief antenatal exposure to glucocorticoids leads to the metabolic syndrome in the offspring. Pregnant marmosets were given the synthetic glucocorticoid dexamethasone orally for 1 week in either early or late gestation, or they were given vehicle. Tissue 11beta-HSD1 and glucocorticoid receptor mRNA expression were examined in the offspring at 4 and 24 months of age. RESULTS: Prenatal dexamethasone administration, selectively during late gestation, resulted in early and persistent elevations in 11beta-HSD1 mRNA expression and activity in the liver, pancreas, and subcutaneous-but not visceral-fat. The increase in 11beta-HSD1 occurred before animals developed obesity or overt features of the metabolic syndrome. In contrast to rodents, in utero dexamethasone exposure did not alter glucocorticoid receptor expression in metabolic tissues in marmosets. CONCLUSIONS: These data suggest that long-term upregulation of 11beta-HSD1 in metabolically active tissues may follow prenatal "stress" hormone exposure and indicates a novel mechanism for fetal origins of adult obesity and the metabolic syndrome

Limits of agricultural greenhouse gas calculators to predict soil N\u3csub\u3e2\u3c/sub\u3eO and CH\u3csub\u3e4\u3c/sub\u3e fluxes in tropical agriculture

Demand for tools to rapidly assess greenhouse gas impacts from policy and technological change in the agricultural sector has catalyzed the development of \u27 GHG calculators\u27-simple accounting approaches that use a mix of emission factors and empirical models to calculate GHG emissions with minimal input data. GHG calculators, however, rely on models calibrated from measurements conducted overwhelmingly under temperate, developed country conditions. Here we show that GHG calculators may poorly estimate emissions in tropical developing countries by comparing calculator predictions against measurements from Africa, Asia, and Latin America. Estimates based on GHG calculators were greater than measurements in 70% of the cases, exceeding twice the measured flux nearly half the time. For 41% of the comparisons, calculators incorrectly predicted whether emissions would increase or decrease with a change in management. These results raise concerns about applying GHG calculators to tropical farming systems and emphasize the need to broaden the scope of the underlying data