Terrestrial natural sources of trichloromethane (chloroform, CHCl3) – An overview

The widespread use of volatile chlorinatedcompounds like chloroform, trichloroethene andtetrachloroethene in industrialized societiescauses a large annual release of thesecompounds into the environment. Due to theirrole as a source for halogen radicals involvedin various catalytic atmospheric reactioncycles, including the regulation of thestratospheric and tropospheric ozone layers,these compounds also constitute a risk fordrinking water resources as they can betransported to the groundwater fromcontaminated field sites or even fromatmospheric deposition. Therefore,identification and investigation of sources andsinks of volatile chlorinated compounds are ofparticular interest. Chloroform, a majorcontributor to natural gaseous chlorine, wasfound to be emitted by several anthropogenicand natural sources including the oceans andterrestrial areas. The origin of chloroform inthe terrestrial environment can beanthropogenic point sources, atmosphericdeposition, release by vegetation andproduction directly in the soil. The calculatedannual biogenic global chloroform emission is700 Gg, and marine and terrestrial environmentsare nearly equal contributors. The estimatedemissions from anthropogenic sources accountfor less than 10% of the estimated totalemissions from all sources. Among terrestrialsources, forests have recently been identifiedas contributing to the release of chloroform intothe environment. With the data available,annual emissions of chloroform to theatmosphere from forest sites were calculatedand compared to other natural sources. Atpresent knowledge, forests are only a minorsource in the total biogenic flux ofchloroform, contributing less than 1% to theannual global atmospheric input. However, itshould be noted that data are available forNorthern temperate forests only. The largetropical forest areas may provide a yet unknowninput of chloroform.     

Conductance measurements for data generation in predictive modeling

Summary The electrical resistance of a growth medium inoculated with bacteria may be automatically recorded throughout an incubation period without the necessity for sampling. The rate of change in conductance is dependent on the bacteria studied, the medium composition and the prevailing growth conditions.The effect of growth medium composition, growth conditions and inoculum level on the conductance response was studied forYersinia enterocolitica O:3. A large number of combinations of factors affecting the growth/activity of the bacteria could be studied simultaneously due to the large instrumental capacity of the Malthus 2000. A polynomial model based on conductance measurements was developed forY. enterocolitica describing the effect of temperature, pH andl-lactate level on conductance response curve parameters. The model was used for predicting growth rates. Growth rates calculated from bacterial counts ofY. enterocolitica growing in minced pork corresponded to growth rates predicted using the polynomial conductance models.     

Identity and stereochemistry of allopurpurin and Tedaniaxanthin

The identity of the carotenoids tedaniaxanthin and allopurpurin from marine sponges has been demonstrated by a direct quantitative comparison of their I₂-catalysed stereomutation mixtures (HPLC and visible spectra). Studies on the geometrical isomerism are reported. The 2R-configuration is assigned on the basis of a CD-correlation of the HPLC-purified all-trans isomer and (3R,3′R)-aloxanthin.     

On the absolute configuration of 19′-hexanoyloxyfucoxanthin

The esterifying C₆-acid in 19′-hexanoyloxyfucoxanthin has been identified as n-hexanoic acid by GLC of the methyl ester. Ozonolysis of 19′-n-hexanoyloxyfucoxanthin 3-benzoate provided the n-hexanoyloxy derivative of the allenic ketone produced from fucoxanthin 3-benzoate. NMR and CD correlation of the ozonolysis products and NMR of the native carotenoids provided the basis for assignment of the same absolute configuration of the 19′-n-hexanoyloxy derivative (3S, 5R, 6S, 3′S, 5′R, 6′S) as for fucoxanthin. Biosynthetic implications are considered. CD data for 19′-n-hexanoyloxyfucoxanthin, fucoxanthin and some derivatives thereof are reported. Previously unreported minor carotenoids in Coccolithus huxleyi were diadinoxanthin and 3′-desacetyl 19′-n-hexanoyloxy-fucoxanthin.     

pH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations

Cytochromes belong to a diverse family of heme-containing redox proteins that function as intermediaries in electron transfer chains. They can be soluble, extrinsic, or intrinsic membrane proteins, and are found in different structural motifs (globin, 4-helix bundles, alpha beta roll, beta sandwich). Measured electrochemical midpoint potentials vary over a wide range even though the basic redox reaction at the heme is the same for all cytochromes. The perturbation of the heme electrochemistry is induced by the protein structure. Also, the pH dependence varies since it depends on the strength of interaction between the heme and surrounding residues as well as the ionization states of these groups. Multiconformation continuum electrostatics (MCCE) has been used to investigate the pH dependence of heme electrochemistry in cytochromes with different folds. Often propionates are the primary contributors for pH dependence especially if they are partially protonated in the reduced heme as it is shown for globin cytochrome c551 P. aeruginosa and cytochrome b5 R. norvegicus (alpha beta roll). However, if the propionates are already fully ionized at a certain pH they do not contribute to the pH dependence even if they have big interaction with the heme. At pH 7 there is no propionate contribution for cytochrome f C. reinhardtii (beta sandwich) and the 4-helix bundle c' R. palustris. Other residues can also change their ionization significantly during heme oxidation and therefore be involved in proton release and pH dependence. These residues have been identified for different cytochrome types.     

Unraveling the mechanism of proton translocation in the extracellular half‐channel of bacteriorhodopsin

Bacteriorhodopsin, a light activated protein that creates a proton gradient in halobacteria, has long served as a simple model of proton pumps. Within bacteriorhodopsin, several key sites undergo protonation changes during the photocycle, moving protons from the higher pH cytoplasm to the lower pH extracellular side. The mechanism underlying the long‐range proton translocation between the central (the retinal Schiff base SB216, D85, and D212) and exit clusters (E194 and E204) remains elusive. To obtain a dynamic view of the key factors controlling proton translocation, a systematic study using molecular dynamics simulation was performed for eight bacteriorhodopsin models varying in retinal isomer and protonation states of the SB216, D85, D212, and E204. The side‐chain orientation of R82 is determined primarily by the protonation states of the residues in the EC. The side‐chain reorientation of R82 modulates the hydrogen‐bond network and consequently possible pathways of proton transfer. Quantum mechanical intrinsic reaction coordinate calculations of proton‐transfer in the methyl guanidinium‐hydronium‐hydroxide model system show that proton transfer via a guanidinium group requires an initial geometry permitting proton donation and acceptance by the same amine. In all the bacteriorhodopsin models, R82 can form proton wires with both the CC and the EC connected by the same amine. Alternatively, rare proton wires for proton transfer from the CC to the EC without involving R82 were found in an O′ state where the proton on D85 is transferred to D212. Proteins 2016; 84:639–654. © 2016 Wiley Periodicals, Inc.     

Affinity and activity of non-native quinones at the QB site of bacterial photosynthetic reaction centers

Purple, photosynthetic reaction centers from Rhodobacter sphaeroides bacteria use ubiquinone (UQ₁₀) as both primary (Q_A) and secondary (Q_B) electron acceptors. Many quinones reconstitute Q_A function, while a few will act as Q_B. Nine quinones were tested for their ability to bind and reconstitute Q_A and Q_B functions. Only ubiquinone (UQ) reconstitutes both functions in the same protein. The affinities of the non-native quinones for the Q_B site were determined by a competitive inhibition assay. The affinities of benzoquinones, naphthoquinone (NQ), and 2-methyl-NQ for the Q_B site are 7 ± 3 times weaker than that at Q_A site. However, di-ortho-substituted NQs and anthraquinone bind tightly to the Q_A site (K _d ≤ 200 nM), and ≥1,000 times more weakly to the Q_B site, perhaps setting a limit on the size of the site. With a low-potential electron donor, 2-methyl, 3-dimethylamino-1,4-NQ, (Me-diMeAm-NQ) at Q_A, Q_B reduction is 260 meV, more favorable than with UQ as Q_A. Electron transfer from Me-diMeAm-NQ at the Q_A site to NQ at the Q_B site can be detected. In the Q_B site, the NQ semiquinone is estimated to be ≈60–100 meV higher in energy than the UQ semiquinone, while in the Q_A site, the semiquinone energy level is similar or lower with NQ than with UQ. Thus, the NQ semiquinone is more stable in the Q_A than in the Q_B site. In contrast, the native UQ semiquinone is ≈60 meV lower in energy in the Q_B than in the Q_A site, stabilizing forward electron transfer from Q_A to Q_B.     

Production of IL-1Ra by human mononuclear blood cells in vitro: influence of serum factors

In vitro cell culture models that measure cytokine production can be of great value when analyzing regulatory mechanisms underlying various pathological conditions. However, testing the function of peripheral blood cells has to take into consideration that serum factors are likely to be of importance in maintaining their function. Interleukin-1 receptor antagonist (IL-1Ra) is a cytokine of key importance in immune regulation and is believed to be involved in numerous pathological processes, such as autoimmunity and cancer. We investigated the influence of normal, human serum on spontaneous production of IL-1Ra by human peripheral blood mononuclear cells (PBMC) in vitro. IL-1Ra production in vitro spanned over a wide range of concentrations, which could be attributed to a combined effect of both cellular parameters and properties of the serum used. The production of IL-1Ra in vitro could be correlated to the level of immobilized IgG, especially IgG1 and IgG3, which is adsorbed from the serum and bound to the tissue culture wells during culture. However, the amount of serum IgG adsorbed to the tissue culture wells could not necessarily be predicted based on the serum concentration of IgG.