Purification and structural characterization of the Na⁺-translocating ferredoxin: NAD⁺ reductase (Rnf) complex of Clostridium tetanomorphum

Various microbial metabolisms use H+/Na+-translocating ferredoxin:NAD+ reductase (Rnf) either to exergonically oxidize reduced ferredoxin by NAD+ for generating a transmembrane electrochemical potential or reversely to exploit the latter for producing reduced ferredoxin. For cryo-EM structural analysis, we elaborated a quick four-step purification protocol for the Rnf complex from Clostridium tetanomorphum and integrated the homogeneous and active enzyme into a nanodisc. The obtained 4.27 Å density map largely allows chain tracing and redox cofactor identification complemented by biochemical data from entire Rnf and single subunits RnfB, RnfC and RnfG. On this basis, we postulated an electron transfer route between ferredoxin and NAD via eight [4Fe-4S] clusters, one Fe ion and four flavins crossing the cell membrane twice related to the pathway of NADH:ubiquinone reductase. Redox-coupled Na+ translocation is provided by orchestrating Na+ uptake/release, electrostatic effects of the assumed membrane-integrated FMN semiquinone anion and accompanied polypeptide rearrangements mediated by different redox steps

Individual behavioural responses of an intermediate host to a manipulative acanthocephalan parasite and the effects of intra-specific parasite competition

© 2018 Timo Thünken. Background: Parasites with complex life cycles depend on the ingestion of their intermediate host by the final host. To complete their life cycle successfully, parasites frequently manipulate the behaviour and appearance of the intermediate host. Within host–parasite systems, there is considerable variation in the intermediate host’s behavioural response to infection. Aim: Identify sources of parasite-induced variation in intermediate hosts’ traits by focusing on intra- and inter-individual variation in behavioural responses to parasitic manipulation, taking infection intensity – and thus parasitic competition – into account. Organism: The acanthocephalan parasite Polymorphus minutus, which alters the phototactic behaviour and activity of its intermediate host, Gammarus pulex, thereby increasing the probability of being eaten by the final host. Methods: We repeatedly examined the behaviour of individual G. pulex varying in intensity of infection with P. minutus from uninfected to multiple-infected. We analysed phototactic responses and activity. Results and conclusions: Individual gammarids differed in phototactic behaviour and in activity patterns, with repeatability ranging from 20% to 50%. Infected gammarids showed greater between-individual variation in phototaxis but not activity than uninfected gammarids. All uninfected gammarids were photophobic, whereas the phototactic behaviour of infected gammarids ranged from photophobia to photophilia. On average, multiple-infected gammarids were similarly photophobic as uninfected ones. Single-infected gammarids were less photophobic than uninfected and multiple-infected conspecifics. This suggests that intra-specific parasitic competition affects the manipulative abilities of parasites. Both groups of infected gammarids were on average less active than uninfected ones, and this effect was mainly driven by some infected individuals. In conclusion, behavioural variation of gammarids was caused both by individual differences in responses to manipulation/infection, and by the reduced manipulative capacities of parasites facing intra-specific competition

Improvement of the Prediction of Surface Ozone Concentration Over Conterminous U.S. by a Computationally Efficient Second-Order Rosenbrock Solver in CAM4-Chem

The global chemistry-climate model (CAM4-Chem) overestimates the surface ozone concentration over the conterminous U.S. (CONUS). Reasons for this positive bias include emission, meteorology, chemical mechanism, and solver. In this study, we explore the last possibility by examining the sensitivity to the numerical methods for solving the chemistry equations. A second-order Rosenbrock (ROS-2) solver is implemented in CAM4-Chem to examine its influence on the surface ozone concentration and the computational performance of the chemistry program. Results show that under the same time step size (1800 s), statistically significant reduction of positive bias is achieved by the ROS-2 solver. The improvement is as large as 5.2 ppb in Eastern U.S. during summer season. The ROS-2 solver is shown to reduce the positive bias in Europe and Asia as well, indicating the lower surface ozone concentration over the CONUS predicted by the ROS-2 solver is not a trade-off consequence with increasing the ozone concentration at other global regions. In addition, by refining the time step size to 180 s, the first-order implicit solver does not provide statistically significant improvement of surface ozone concentration. It reveals that the better prediction from the ROS-2 solver is not only due to its accuracy but also due to its suitability for stiff chemistry equations. As an added benefit, the computation cost of the ROS-2 solver is almost half of first-order implicit solver. The improved computational efficiency of the ROS-2 solver is due to the reuse of the Jacobian matrix and lower upper (LU) factorization during its multistage calculation

Ecology of Alopoglossus angulatus and A. atriventris (Squamata, Gymnophthalmidae) in western Amazonia

We studied the ecology of Alopoglossus angulatus and A. atriventris in western Amazonia. Both species are found in leaf litter of lowland tropical forest, but A. angulatus tends to be found near water whereas A. atriventris is found in terra firme forest. Both tend to be active in shade on sunny and cloudy days. Body size of adults differs (A. angulatus larger), but species differences in sizeadjusted morphology are minor. Sexual dimorphism exists in relative head length (males larger) only in A. atriventris. Diets are similar, with roaches, spiders, grasshoppers/crickets, and springtails dominating the diet. Overall, these lizards are similar ecologically even though they occur together at many sites. Leaf litter and shaded forest appear to be requisites for survival at the local level

A comparison of electrochemical degradation of phenol on boron doped diamond and lead dioxide anodes

This work compares two electrode materials used to mineralize phenol contained in waste waters. Two disks covered with either boron doped diamond (BDD) or PbO2 were used as anodes in a one compartment flow cell under the same hydrodynamic conditions. Efficiencies of galvanostatic electrolyses are compared on the basis of measurements of Total Organic Carbon (TOC) and Chemical Oxygen Demand (COD). Galvanostatic electrolyses were monitored by analysis of phenol and of its oxidation derivatives to evaluate the operating time needed for complete elimination of toxic aromatics. The experimental current efficiency is close to the theoretical value for the BDD electrode. Other parameters being equal, phenol species disappeared at the same rate using the two electrode materials but the BDD anode showed better efficiency to eliminate TOC and COD. Moreover, during the electrolysis less intermediates are formed with BDD compared to PbO2 whatever the current density. A comparison of energy consumption is given based on the criterion of 99% removal of aromatic compounds

Description and evaluation of tropospheric chemistry and aerosols in the Community Earth System Model (CESM1.2)

The Community Atmosphere Model (CAM), version 5, is now coupled to extensive tropospheric and stratospheric chemistry, called CAM5-chem, and is available in addition to CAM4-chem in the Community Earth System Model (CESM) version 1.2. The main focus of this paper is to compare the performance of configurations with internally derived "free running" (FR) meteorology and "specified dynamics" (SD) against observations from surface, aircraft, and satellite, as well as understand the origin of the identified differences. We focus on the representation of aerosols and chemistry. All model configurations reproduce tropospheric ozone for most regions based on in situ and satellite observations. However, shortcomings exist in the representation of ozone precursors and aerosols. Tropospheric ozone in all model configurations agrees for the most part with ozonesondes and satellite observations in the tropics and the Northern Hemisphere within the variability of the observations. Southern hemispheric tropospheric ozone is consistently underestimated by up to 25%. Differences in convection and stratosphere to troposphere exchange processes are mostly responsible for differences in ozone in the different model configurations. Carbon monoxide (CO) and other volatile organic compounds are largely underestimated in Northern Hemisphere mid-latitudes based on satellite and aircraft observations. Nitrogen oxides (NOx) are biased low in the free tropical troposphere, whereas peroxyacetyl nitrate (PAN) is overestimated in particular in high northern latitudes. The present-day methane lifetime estimates are compared among the different model configurations. These range between 7.8 years in the SD configuration of CAM5-chem and 8.8 years in the FR configuration of CAM4-chem and are therefore underestimated compared to observational estimations. We find that differences in tropospheric aerosol surface area between CAM4 and CAM5 play an important role in controlling the burden of the tropical tropospheric hydroxyl radical (OH), which causes differences in tropical methane lifetime of about half a year between CAM4-chem and CAM5-chem. In addition, different distributions of NOx from lightning explain about half of the difference between SD and FR model versions in both CAM4-chem and CAM5-chem. Remaining differences in the tropical OH burden are due to enhanced tropical ozone burden in SD configurations compared to the FR versions, which are not only caused by differences in chemical production or loss but also by transport and mixing. For future studies, we recommend the use of CAM5-chem configurations, due to improved aerosol description and inclusion of aerosol–cloud interactions. However, smaller tropospheric surface area density in the current version of CAM5-chem compared to CAM4-chem results in larger oxidizing capacity in the troposphere and therefore a shorter methane lifetime

Representation of the Community Earth System Model (CESM1) CAM4-chem within the Chemistry-Climate Model Initiative (CCMI)

The Community Earth System Model (CESM1) CAM4-chem has been used to perform the Chemistry Climate Model Initiative (CCMI) reference and sensitivity simulations. In this model, the Community Atmospheric Model version 4 (CAM4) is fully coupled to tropospheric and stratospheric chemistry. Details and specifics of each configuration, including new developments and improvements are described. CESM1 CAM4-chem is a low-top model that reaches up to approximately 40km and uses a horizontal resolution of 1.9° latitude and 2.5° longitude. For the specified dynamics experiments, the model is nudged to Modern-Era Retrospective Analysis for Research and Applications (MERRA) reanalysis. We summarize the performance of the three reference simulations suggested by CCMI, with a focus on the last 15 years of the simulation when most observations are available. Comparisons with selected data sets are employed to demonstrate the general performance of the model. We highlight new data sets that are suited for multi-model evaluation studies. Most important improvements of the model are the treatment of stratospheric aerosols and the corresponding adjustments for radiation and optics, the updated chemistry scheme including improved polar chemistry and stratospheric dynamics and improved dry deposition rates. These updates lead to a very good representation of tropospheric ozone within 20% of values from available observations for most regions. In particular, the trend and magnitude of surface ozone is much improved compared to earlier versions of the model. Furthermore, stratospheric column ozone of the Southern Hemisphere in winter and spring is reasonably well represented. All experiments still underestimate CO most significantly in Northern Hemisphere spring and show a significant underestimation of hydrocarbons based on surface observations

Atmospheric Acetaldehyde: Importance of Air-Sea Exchange and a Missing Source in the Remote Troposphere.

We report airborne measurements of acetaldehyde (CH3CHO) during the first and second deployments of the National Aeronautics and Space Administration (NASA) Atmospheric Tomography Mission (ATom). The budget of CH3CHO is examined using the Community Atmospheric Model with chemistry (CAM-chem), with a newly-developed online air-sea exchange module. The upper limit of the global ocean net emission of CH3CHO is estimated to be 34 Tg a-1 (42 Tg a-1 if considering bubble-mediated transfer), and the ocean impacts on tropospheric CH3CHO are mostly confined to the marine boundary layer. Our analysis suggests that there is an unaccounted CH3CHO source in the remote troposphere and that organic aerosols can only provide a fraction of this missing source. We propose that peroxyacetic acid (PAA) is an ideal indicator of the rapid CH3CHO production in the remote troposphere. The higher-than-expected CH3CHO measurements represent a missing sink of hydroxyl radicals (and halogen radical) in current chemistry-climate models

Relationship between ecosystem productivity and photosynthetically-active radiation for northern peatlands

We analyzed the relationship between net ecosystem exchange of carbon dioxide (NEE) and irradiance (as photosynthetic photon flux density or PPFD), using published and unpublished data that have been collected during midgrowing season for carbon balance studies at seven peatlands in North America and Europe. NEE measurements included both eddy-correlation tower and clear, static chamber methods, which gave very similar results. Data were analyzed by site, as aggregated data sets by peatland type (bog, poor fen, rich fen, and all fens) and as a single aggregated data set for all peatlands. In all cases, a fit with a rectangular hyperbola (NEE = α PPFD Pmax/(α PPFD + Pmax) + R) better described the NEE-PPFD relationship than did a linear fit (NEE = β PPFD + R). Poor and rich fens generally had similar NEE-PPFD relationships, while bogs had lower respiration rates (R = −2.0μmol m−2s−1 for bogs and −2.7 μmol m−2s−1 for fens) and lower NEE at moderate and high light levels (Pmax = 5.2 μmol m−2s−1 for bogs and 10.8 μmol m−2s−1 for fens). As a single class, northern peatlands had much smaller ecosystem respiration (R = −2.4 μmol m−2s−1) and NEE rates (α = 0.020 and Pmax = 9.2μmol m−2s−1) than the upland ecosystems (closed canopy forest, grassland, and cropland) summarized by Ruimy et al. [1995]. Despite this low productivity, northern peatland soil carbon pools are generally 5–50 times larger than upland ecosystems because of slow rates of decomposition caused by litter quality and anaerobic, cold soils

Global patterns of body size evolution are driven by precipitation in legless amphibians

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordBody size shapes ecological interactions across and within species, ultimately influencing the evolution of large-scale biodiversity patterns. Therefore, macroecological studies of body size provide a link between spatial variation in selection regimes and the evolution of animal assemblages through space. Multiple hypotheses have been formulated to explain the evolution of spatial gradients of animal body size, predominantly driven by thermal (Bergmann's rule), humidity (‘water conservation hypothesis’) and resource constraints (‘resource rule’, ‘seasonality rule’) on physiological homeostasis. However, while integrative tests of all four hypotheses combined are needed, the focus of such empirical efforts needs to move beyond the traditional endotherm–ectotherm dichotomy, to instead interrogate the role that variation in lifestyles within major lineages (e.g. classes) play in creating neglected scenarios of selection via analyses of largely overlooked environment–body size interactions. Here, we test all four rules above using a global database spanning 99% of modern species of an entire Order of legless, predominantly underground-dwelling amphibians (Gymnophiona, or caecilians). We found a consistent effect of increasing precipitation (and resource abundance) on body size reductions (supporting the water conservation hypothesis), while Bergmann's, the seasonality and resource rules are rejected. We argue that subterranean lifestyles minimize the effects of aboveground selection agents, making humidity a dominant selection pressure – aridity promotes larger body sizes that reduce risk of evaporative dehydration, while smaller sizes occur in wetter environments where dehydration constraints are relaxed. We discuss the links between these principles with the physiological constraints that may have influenced the tropically-restricted global radiation of caecilians.Natural Environment Research Council (NERC)O2National Lottery - Big Lottery Fun