Arsenicicoccus bolidensis a novel arsenic reducing actinomycete in contaminated sediments near the Adak mine (northern Sweden): impact on water chemistry

Weathering of mine tailings in Adak results in high As concentrations in surface and ground water, sediments, and soil. In spite of the oxic conditions, As-rich surface and ground, water samples indicate As(III) species predominantly (up to 83%). Several microorganisms were isolated from the enrichment cultures that were involved in As cycling. Amongst them was Arsenicicoccus bolidensis - a novel gram-positive, facultatively anaerobic, coccus-shaped actinomycete, which actively reduced As(V) to As(III) in aqueous media. A. bolidensis reduced 0.06-0.20 mM day(-1) As(V). As(V) reduction displays a direct correlation between the initial As(V) concentration, growth rate, and biomass yield. (c) 2006 Elsevier B.V. All rights reserved.

Recent highlights in modified oligonucleotide chemistry

The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modi. cations to the base portion will be discussed followed secondly by modi. cations to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids ( PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.

Flux difference splitting for inviscid, real gases with non-equilibrium chemistry

A flux-difference splitting method is presented for the inviscid terms of the compressible flow equations for chemical non-equilibrium gases

A finite difference scheme for inviscid flows with non-eequilibrium chemistry and internal energy

A finite difference scheme is presented for the inviscid terms of the equations of compressible fluid dynamics with general non-equilibrium chemistry and internal energy.

Chemistry and biology of maculalactone A from the marine cyanobacterium Kyrtuthrix maculans

Maculalactone A is the most abundant secondary metabolite in Kyrtuthrix maculans, a marine cyanobacterium found in the mid-high shore of moderately exposed to sheltered rocky shores in Hong Kong and South East Asia. This species appears to survive as pure colonies forming distinct black zones on the rock. Maculalactone A may provide K. maculans with a chemical defense against several marine organisms, including the common grazer, Chlorostoma argyrostoma and settlement by larvae of the barnacles, Tetraclita japonica, Balanus amphitrite and Ibla cumingii. The natural concentration of maculalactone A varied with season and also with tidal height on the shore and although a strong positive linear correlation was observed between maculalactone A concentration and herbivore grazing pressure, manipulative experiments demonstrated that grazing pressure was not directly responsible for inducing the biosynthesis of this metabolite. The potential of maculalactone A as a natural marine anti-fouling agent (i.e. as an alternative to environmentally-damaging copper- and tin-based anti-fouling paints) was investigated after achieving a gram-scale synthesis of this compound. Preliminary field trials with anti-fouling paints which contained synthetic maculalactone A as the active principle have confirmed that this compound seems to have a specific activity against molluscan settlers.

Precipitation and latent heating distributions from satellite passive microwave radiometry. Part I: improved method and uncertainties

A revised Bayesian algorithm for estimating surface rain rate, convective rain proportion, and latent heating profiles from satellite-borne passive microwave radiometer observations over ocean backgrounds is described. The algorithm searches a large database of cloud-radiative model simulations to find cloud profiles that are radiatively consistent with a given set of microwave radiance measurements. The properties of these radiatively consistent profiles are then composited to obtain best estimates of the observed properties. The revised algorithm is supported by an expanded and more physically consistent database of cloud-radiative model simulations. The algorithm also features a better quantification of the convective and nonconvective contributions to total rainfall, a new geographic database, and an improved representation of background radiances in rain-free regions. Bias and random error estimates are derived from applications of the algorithm to synthetic radiance data, based upon a subset of cloud-resolving model simulations, and from the Bayesian formulation itself. Synthetic rain-rate and latent heating estimates exhibit a trend of high (low) bias for low (high) retrieved values. The Bayesian estimates of random error are propagated to represent errors at coarser time and space resolutions, based upon applications of the algorithm to TRMM Microwave Imager (TMI) data. Errors in TMI instantaneous rain-rate estimates at 0.5°-resolution range from approximately 50% at 1 mm h−1 to 20% at 14 mm h−1. Errors in collocated spaceborne radar rain-rate estimates are roughly 50%–80% of the TMI errors at this resolution. The estimated algorithm random error in TMI rain rates at monthly, 2.5° resolution is relatively small (less than 6% at 5 mm day−1) in comparison with the random error resulting from infrequent satellite temporal sampling (8%–35% at the same rain rate). Percentage errors resulting from sampling decrease with increasing rain rate, and sampling errors in latent heating rates follow the same trend. Averaging over 3 months reduces sampling errors in rain rates to 6%–15% at 5 mm day−1, with proportionate reductions in latent heating sampling errors.

Bayesian retrieval of complete posterior PDFs of oceanic rain rate from microwave observations

A new Bayesian algorithm for retrieving surface rain rate from Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) over the ocean is presented, along with validations against estimates from the TRMM Precipitation Radar (PR). The Bayesian approach offers a rigorous basis for optimally combining multichannel observations with prior knowledge. While other rain-rate algorithms have been published that are based at least partly on Bayesian reasoning, this is believed to be the first self-contained algorithm that fully exploits Bayes’s theorem to yield not just a single rain rate, but rather a continuous posterior probability distribution of rain rate. To advance the understanding of theoretical benefits of the Bayesian approach, sensitivity analyses have been conducted based on two synthetic datasets for which the “true” conditional and prior distribution are known. Results demonstrate that even when the prior and conditional likelihoods are specified perfectly, biased retrievals may occur at high rain rates. This bias is not the result of a defect of the Bayesian formalism, but rather represents the expected outcome when the physical constraint imposed by the radiometric observations is weak owing to saturation effects. It is also suggested that both the choice of the estimators and the prior information are crucial to the retrieval. In addition, the performance of the Bayesian algorithm herein is found to be comparable to that of other benchmark algorithms in real-world applications, while having the additional advantage of providing a complete continuous posterior probability distribution of surface rain rate.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Coupled chemistry climate model simulations of stratospheric temperatures and their trends for the recent past

Temperature results from multi-decadal simulations of coupled chemistry climate models for the recent past are analyzed using multi-linear regression including a trend, solar cycle, lower stratospheric tropical wind, and volcanic aerosol terms. The climatology of the models for recent years is in good agreement with observations for the troposphere but the model results diverge from each other and from observations in the stratosphere. Overall, the models agree better with observations than in previous assessments, primarily because of corrections in the observed temperatures. The annually averaged global and polar temperature trends simulated by the models are generally in agreement with revised satellite observations and radiosonde data over much of their altitude range. In the global average, the model trends underpredict the radiosonde data slightly at the top of the observed range. Over the Antarctic some models underpredict the temperature trend in the lower stratosphere, while others overpredict the trends

Long-lived halocarbon trends and budgets from atmospheric chemistry modelling constrained with measurements in polar firn

The budgets of seven halogenated gases (CFC-11, CFC-12, CFC-113, CFC-114, CFC-115, CCl4 and SF6) are studied by comparing measurements in polar firn air from two Arctic and three Antarctic sites, and simulation results of two numerical models: a 2-D atmospheric chemistry model and a 1-D firn diffusion model. The first one is used to calculate atmospheric concentrations from emission trends based on industrial inventories; the calculated concentration trends are used by the second one to produce depth concentration profiles in the firn. The 2-D atmospheric model is validated in the boundary layer by comparison with atmospheric station measurements, and vertically for CFC-12 by comparison with balloon and FTIR measurements. Firn air measurements provide constraints on historical atmospheric concentrations over the last century. Age distributions in the firn are discussed using a Green function approach. Finally, our results are used as input to a radiative model in order to evaluate the radiative forcing of our target gases. Multi-species and multi-site firn air studies allow to better constrain atmospheric trends. The low concentrations of all studied gases at the bottom of the firn, and their consistency with our model results confirm that their natural sources are small. Our results indicate that the emissions, sinks and trends of CFC-11, CFC-12, CFC-113, CFC-115 and SF6 are well constrained, whereas it is not the case for CFC-114 and CCl4. Significant emission-dependent changes in the lifetimes of halocarbons destroyed in the stratosphere were obtained. Those result from the time needed for their transport from the surface where they are emitted to the stratosphere where they are destroyed. Efforts should be made to update and reduce the large uncertainties on CFC lifetimes.

Exploring NOy chemistry in levitated aqueous aerosol droplets

Chemistry of reactive nitrogen oxides, NOy, is crucial for our understanding of composition and properties of the Earth’s atmosphere. The proof-of-principle experiments demonstrated that we are able to study the atmospheric fate of nitrogen oxides that has significant impact on global climate and hydrological cycle, thus affecting the likelihood of local floods and acid rain.

Coupling aerosol surface and bulk chemistry with a kinetic double layer model (K2-SUB): oxidation of oleic acid by ozone

We present a kinetic double layer model coupling aerosol surface and bulk chemistry (K2-SUB) based on the PRA framework of gas-particle interactions (Poschl-Rudich-Ammann, 2007). K2-SUB is applied to a popular model system of atmospheric heterogeneous chemistry: the interaction of ozone with oleic acid. We show that our modelling approach allows de-convoluting surface and bulk processes, which has been a controversial topic and remains an important challenge for the understanding and description of atmospheric aerosol transformation. In particular, we demonstrate how a detailed treatment of adsorption and reaction at the surface can be coupled to a description of bulk reaction and transport that is consistent with traditional resistor model formulations. From literature data we have derived a consistent set of kinetic parameters that characterise mass transport and chemical reaction of ozone at the surface and in the bulk of oleic acid droplets. Due to the wide range of rate coefficients reported from different experimental studies, the exact proportions between surface and bulk reaction rates remain uncertain. Nevertheless, the model results suggest an important role of chemical reaction in the bulk and an approximate upper limit of similar to 10(-11) cm(2) s(-1) for the surface reaction rate coefficient. Sensitivity studies show that the surface accommodation coefficient of the gas-phase reactant has a strong non-linear influence on both surface and bulk chemical reactions. We suggest that K2-SUB may be used to design, interpret and analyse future experiments for better discrimination between surface and bulk processes in the oleic acid-ozone system as well as in other heterogeneous reaction systems of atmospheric relevance.