Role of pili and the phase-variable PilC protein in natural competence for transformation of Neisseria gonorrhoeae.

The Gram-negative bacterial pathogen Neisseria gonorrhoeae is naturally competent for transformation with species-related DNA. We show here that two phase-variable pilus-associated proteins, the major pilus subunit (pilin, or PilE) and PilC, a factor known to function in the assembly and adherence of gonococcal pili, are essential for transformation competence. The PilE and PilC proteins are necessary for the conversion of linearized plasmid DNA carrying the Neisseria-specific DNA uptake signal into a DNase-resistant form. The biogenesis of typical pilus fibers is neither essential nor sufficient for this process. DNA uptake deficiency of defined piliated pilC1,2 double mutants can be complemented by expression of a cloned pilC2 gene in trans. The PilC defect can also be restored by the addition of purified PilC protein, or better, pili containing PilC protein, to the mutant gonococci. Our data suggest that the two phase-variable Pil proteins act on the bacterial cell surface and cooperate in DNA recognition and/or outer membrane translocation.

Australian water mass variations from GRACE data linked to Indo-Pacific climate variability

Time-variable gravity data from the Gravity Recovery And Climate Experiment (GRACE) mission are used to study total water content over Australia for the period 2002–2010. A time-varying annual signal explains 61% of the variance of the data, in good agreement with two independent estimates of the same quantity from hydrological models. Water mass content variations across Australia are linked to Pacific and Indian Ocean variability, associated with El Niño-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD), respectively. From 1989, positive (negative) IOD phases were related to anomalously low (high) precipitation in southeastern Australia, associated with a reduced (enhanced) tropical moisture flux. In particular, the sustained water mass content reduction over central and southern regions of Australia during the period 2006–2008 is associated with three consecutive positive IOD events.

The supergiant B[e] star LHA 115-S 18 - binary and/or luminous blue variable?

Context. The mechanism by which supergiant (sg)B[e] stars support cool, dense dusty discs/tori and their physical relationship with other evolved, massive stars such as luminous blue variables is uncertain. Aims. In order to investigate both issues we have analysed the long term behaviour of the canonical sgB[e] star LHA 115-S 18. Methods. We employed the OGLE II-IV lightcurve to search for (a-)periodic variability and supplemented these data with new and historic spectroscopy. Results. In contrast to historical expectations for sgB[e] stars, S18 is both photometrically and spectroscopically highly variable. The lightcurve is characterised by rapid aperiodic ` aring' throughout the 16 years of observations. Changes in the high excitation emission line component of the spectrum imply evolution in the stellar temperature - as expected for luminous blue variables - although somewhat surprisingly, spectroscopic and photometric variability appears not to be correlated. Characterised by emission in low excitation metallic species, the cool circumstellar torus appears largely unaffected by this behaviour. Finally, in conjunction with intense, highly variable He ii emission, X-ray emission implies the presence of an unseen binary companion. Conclusions. S18 provides observational support for the putative physical association of (a subset of) sgB[e] stars and luminous blue variables. Given the nature of the circumstellar environment of S18 and that luminous blue variables have been suggested as SN progenitors, it is tempting to draw a parallel to the progenitors of SN1987A and SN2009ip. Moreover the likely binary nature of S18 strengthens the possibility that the dusty discs/tori that characterise sgB[e] stars are the result of binary-driven mass-loss; consequently such stars may provide a window on the short lived phase of mass-transfer in massive compact binaries.

A data driven study of relationships between relief and farmland abandonment in a Mediterranean region

The environmental, cultural and socio-economic causes and consequences of farmland abandonment are issues of increasing concern for researchers and policy makers. In previous studies, we proposed a new methodology for selecting the driving factors in farmland abandonment processes. Using Data Mining and GIS, it is possible to select those variables which are more significantly related to abandonment. The aim of this study is to investigate the application of the above mentioned methodology for finding relationships between relief and farmland abandonment in a Mediterranean region (SE Spain).We have taken into account up to 28 different variables in a single analysis, some of them commonly considered in land use change studies (slope, altitude, TWI, etc), but also other novel variables have been evaluated (sky view factor, terrain view factor, etc). The variable selection process provides results in line with the previous knowledge of the study area, describing some processes that are region specific (e.g. abandonment versus intensification of the agricultural activities). The European INSPIRE Directive (2007/2/EC) establishes that the digital elevation models for land surfaces should be available in all member countries, this means that the research described in this work can be extrapolated to any European country to determine whether these variables (slope, altitude, etc) are important in the process of abandonment.

On the decorrelation filtering of RL05 GRACE data for global applications

In autumn 2012, the new release 05 (RL05) of monthly geopotencial spherical harmonics Stokes coefficients (SC) from GRACE (Gravity Recovery and Climate Experiment) mission was published. This release reduces the noise in high degree and order SC, but they still need to be filtered. One of the most common filtering processing is the combination of decorrelation and Gaussian filters. Both of them are parameters dependent and must be tuned by the users. Previous studies have analyzed the parameters choice for the RL05 GRACE data for oceanic applications, and for RL04 data for global application. This study updates the latter for RL05 data extending the statistics analysis. The choice of the parameters of the decorrelation filter has been optimized to: (1) balance the noise reduction and the geophysical signal attenuation produced by the filtering process; (2) minimize the differences between GRACE and model-based data; (3) maximize the ratio of variability between continents and oceans. The Gaussian filter has been optimized following the latter criteria. Besides, an anisotropic filter, the fan filter, has been analyzed as an alternative to the Gauss filter, producing better statistics.

System Costs of Variable Renewable Energy in the European Union. Bruges European Economic Policy (BEEP) Briefings 37/2015

To shift to a low-carbon economy, the EU has been encouraging the deployment of variable renewable energy sources (VRE). However, VRE lack of competitiveness and their technical specificities have substantially raised the cost of the transition. Economic evaluations show that VRE life-cycle costs of electricity generation are still today higher than those of conventional thermal power plants. Member States have consequently adopted dedicated policies to support them. In addition, Ueckerdt et al. (2013) show that when integrated to the power system, VRE induce supplementary not-accounted-for costs. This paper first exposes the rationale of EU renewables goals, the EU targets and current deployment. It then explains why the LCOE metric is not appropriate to compute VRE costs by describing integration costs, their magnitude and their implications. Finally, it analyses the consequences for the power system and policy options. The paper shows that the EU has greatly underestimated VRE direct and indirect costs and that policymakers have failed to take into account the burden caused by renewable energy and the return of State support policies. Indeed, induced market distortions have been shattering the whole power system and have undermined competition in the Internal Energy Market. EU policymakers can nonetheless take full account of this negative trend and reverse it by relying on competition rules, setting-up a framework to collect robust EU-wide data, redesigning the architecture of the electricity system and relying on EU regulators.

MGOF: Stata module to perform goodness-of-fit tests for multinomial data

mgof computes goodness-of-fit tests for the distribution of a discrete (categorical, multinomial) variable. The default is to perform classical large sample chi-squared approximation tests based on Pearson's X2 statistic and the log likelihood ratio (G2) statistic or a statistic from the Cressie-Read family. Alternatively, mgof computes exact tests using Monte Carlo methods or exhaustive enumeration. A Kolmogorov-Smirnov test for discrete data is also provided. The moremata package, also available from SSC, is required.

RELRANK: Stata module to generate relative data (grade transformation)

relrank generates the so called (quasi-) relative data of a variable compared to an empirical reference distribution. This is also called the grade transformation.

Organic carbon, calcium carbonate and carbon/nitrogen ratio at DSDP Leg 93 sites

A large number of samples of nonlithified and lithified sediments from Leg 93 sites were analyzed for their contents of organic carbon and calcium carbonate. An average of two samples was selected from every core for carbonate determination; organic carbon was measured in most of these samples. Nearly all of these analyses were performed on board Glomar Challenger for samples from Sites 603 and 604. Site 605 samples, plus some of the deeper samples from Hole 603B, were analyzed at the University of Michigan. The procedures used in both cases were virtually the same, and their results compared well. Organic carbon analyses were done using a Hewlett- Packard 185-B CHN Analyzer. Portions of samples selected for calcium carbonate determinations were treated with dilute HC1 to remove carbonate, washed with deionized water, and dried at 110°C. A Cahn Electrobalance was used to weight 20-mg samples of sediment for CHN analysis. Samples were combusted at 1050°C in the presence of an oxidant, and the volumes of the evolved gases determined as measures of the C, H, and N contents of sediment organic matter. Areas of gas peaks were determined and compared to those of rock standards of known carbon and nitrogen contents. These values were used to standardize instrument response so that C/N atomic ratios could be reported. Organic carbon concentrations were calculated on the basis of sediment dry weight. Hydrogen elemental analysis with the procedure used is untrustworthy because of the variable amounts of clay minerals and their hydrates, hence hydrogen values are not reported for samples analyzed by this method.

Sinking rates of particles measured from deployments in the Atlantic Ocean based on seasonal data

The flux of materials to the deep sea is dominated by larger, organic-rich particles with sinking rates varying between a few meters and several hundred meters per day. Mineral ballast may regulate the transfer of organic matter and other components by determining the sinking rates, e.g. via particle density. We calculated particle sinking rates from mass flux patterns and alkenone measurements applying the results of sediment trap experiments from the Atlantic Ocean. We have indication for higher particle sinking rates in carbonate-dominated production systems when considering both regional and seasonal data. During a summer coccolithophorid bloom in the Cape Blanc coastal upwelling off Mauritania, particle sinking rates reached almost 570 m per day, most probably due the fast sedimentation of densely packed zooplankton fecal pellets, which transport high amounts of organic carbon associated with coccoliths to the deep ocean despite rather low production. During the recurring winter-spring blooms off NW Africa and in opal-rich production systems of the Southern Ocean, sinking rates of larger particles, most probably diatom aggregates, showed a tendency to lower values. However, there is no straightforward relationship between carbonate content and particle sinking rates. This could be due to the unknown composition of carbonate and/or the influence of particle size and shape on sinking rates. It also remains noticeable that the highest sinking rates occurred in dust-rich ocean regions off NW Africa, but this issue deserves further detailed field and laboratory investigations. We obtained increasing sinking rates with depth. By using a seven-compartment biogeochemical model, it was shown that the deep ocean organic carbon flux at a mesotrophic sediment trap site off Cape Blanc can be captured fairly well using seasonal variable particle sinking rates. Our model provides a total organic carbon flux of 0.29 Tg per year down to 3000 m off the NW African upwelling region between 5 and 35° N. Simple parameterisations of remineralisation and sinking rates in such models, however, limit their capability in reproducing the flux variation in the water column.

Stable hydrogen and carbon isotope records and concentration data for four long chain n-alkanes from core GIK16160-3 derived from the Zambezi delta in the Mozambique Channel during the last 37,000 years

Hydrogen isotope values (dD) of sedimentary terrestrial leaf wax such as n-alkanes or n-acids have been used to map and understand past changes in rainfall amount in the tropics because dD of precipitation is commonly assumed as the first order controlling factor of leaf wax dD. Plant functional types and their photosynthetic pathways can also affect leaf wax dD but these biological effects are rarely taken into account in paleo studies relying on this rainfall proxy. To investigate how biological effects may influence dD values we here present a 37,000-year old record of dD and stable carbon isotopes (d13C) measured on four n-alkanes (n-C27, n-C29, n-C31, n-C33) from a marine sediment core collected off the Zambezi River mouth. Our paleo d13C records suggest that each individual n-alkanes had different C3/C4 proportional contributions. n-C29 was mostly derived from a C3 dicots (trees, shrubs and forbs) dominant vegetation throughout the entire record. In contrast, the longer chain n-C33 and n-C31 were mostly contributed by C4 grasses during the Glacial period but shifted to a mixture of C4 grasses and C3 dicots during the Holocene. Strong correlations between dD and d13C values of n-C33 (correlation coefficient R2 = 0.75, n = 58) and n-C31 (R2 = 0.48, n = 58) suggest that their dD values were strongly influenced by changes in the relative contributions of C3/C4 plant types in contrast to n-C29 (R2 = 0.07, n = 58). Within regions with variable C3/C4 input, we conclude that dD values of n-C29 are the most reliable and unbiased indicator for past changes in rainfall, and that dD and d13C values of n-C31 and n-C33 are sensitive to C3/C4 vegetation changes. Our results demonstrate that a robust interpretation of palaeohydrological data using n-alkane dD requires additional knowledge of regional vegetation changes from which nalkanes are synthesized, and that the combination of dD and d13C values of multiple n-alkanes can help to differentiate biological effects from those related to the hydrological cycle.