Redox Properties of the Membrane Proteins from the Respiratory Chain.

This review focuses on the electrochemical and spectroelectrochemical studies that gave insight into redox potentials of the four mitochondrial complexes and their homologues from bacterial respiratory chains using O2 as a terminal acceptor, thus providing crucial information about their reaction mechanism. Advantages and limitations of the use of the different techniques for the study of membrane proteins are presented. Electrocatalytic experiments are described that revealed specific features of the reaction with the substrates and inhibitors. An overview is given on the great variability of the redox and catalytic properties of the enzymes in different organisms that may be due to adaptation to the specific environments in which these enzymes function. The adaptation of the redox chain to the different types of quinone and substrates is analyzed, and future studies are discussed.

Stabilization of the Highly Hydrophobic Membrane Protein, Cytochrome bd Oxidase, on Metallic Surfaces for Direct Electrochemical Studies.

The cytochrome bd oxidase catalyzes the reduction of oxygen to water in bacteria and it is thus an interesting target for electrocatalytic studies and biosensor applications. The bd oxidase is completely embedded in the phospholipid membrane. In this study, the variation of the surface charge of thiol-modified gold nanoparticles, the length of the thiols and the other crucial parameters including optimal phospholipid content and type, have been performed, giving insight into the role of these factors for the optimal interaction and direct electron transfer of an integral membrane protein. Importantly, all three tested factors, the lipid type, the electrode surface charge and the thiol length mutually influenced the stability of films of the cytochrome bd oxidase. The best electrocatalytic responses were obtained on the neutral gold surface when the negatively charged phosphatidylglycerol (PG) was used and on the charged gold surface when the zwitterionic phosphatidylethanolamine (PE) was used. The advantages of the covalent binding of the membrane protein to the electrode surface over the non-covalent binding are also discussed.

Chemical and Electrochemical Alkali Cations Intercalation/Release in an Ionic Hydrogen Bonded Network.

The chemical oxidation of a hydrogen bonded network, formed upon combination of a hydrogen bond donor dication (12+, a dicationic bis-amidinium organic moiety bearing four propyl chains) with [FeIII/II(CN)6]3-/4- anions has been studied using vibrational spectroscopies. The postsynthetic oxidation of the microcrystalline powder of X213-[FeII(CN)6]2 (X = Na, K, and Cs) by S2O82- into 13-[FeIII(CN)6]2 appeared to be partial for X = K+ and Cs+ and total for Na213-[FeII(CN)6]2. It corresponds to a two-step process involving a second order reaction. The reaction time appears to be dependent on the nature of the alkali cation and is faster for X = Na+. The integrity of the hydrogen bonded network, after oxidation, was also confirmed by powder X-ray diffraction. The flexible nature of the hydrogen bonded network allows alkali cation motions within the network during the oxidation process. In addition, the investigation of the electrochemical behavior evidenced an amorphous deposition on a gold electrode immersed into a solution containing (12+ and [FeIII(CN)6]3-) after 100 cycles. This is the first evidence of an electrochemical ion intercalation for a molecular hydrogen bonded network.

An Ocean-Colour Time Series for Use in Climate Studies: The Experience of the Ocean-Colour Climate Change Initiative (OC-CCI).

Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.

On the minimization of adjacency effects in SeaWiFS primary data products from coastal areas.

The minimization of adjacency effects (AE) in SeaWiFS primary products at the Aqua Alta Oceanographic Tower (AAOT) was investigated using sample images concurrent with in situ measurements. The validation exercise was performed with the NASA SeaDAS processing scheme ingesting original SeaWiFS data and alternatively SeaWiFS top-of-atmosphere data corrected for AE, and additionally including and excluding the default turbid water (TW) correction algorithm. Results show overestimates of the TW contributions partially compensating for AE. The analysis also suggests that intra-annual biases observed in SeaWiFS radiometric products at the AAOT may result from a misinterpretation of the NIR atmospheric signal as water contribution in data acquired in winter, and from uncompensated AE in data acquired in summer.

The unusual redox properties of C-type oxidases.

Cytochrome cbb3 (also known as C-type) oxidases belong to the family of heme-copper terminal oxidases which couple at the end of the respiratory chain the reduction of molecular oxygen into water and the pumping of protons across the membrane. They are expressed most often at low pressure of O2 and they exhibit a low homology of sequence with the cytochrome aa3 (A-type) oxidases found in mitochondria. Their binuclear active site comprises a high-spin heme b3 associated with a CuB center. The protein also contains one low-spin heme b and 3 hemes c. We address here the redox properties of cbb3 oxidases from three organisms, Rhodobacter sphaeroides, Vibrio cholerae and Pseudomonas stutzeri by means of electrochemical and spectroscopic techniques. We show that the redox potential of the heme b3 exhibits a relatively low midpoint potential, as in related cytochrome c-dependent nitric oxide reductases. Potential implications for the coupled electron transfer and proton uptake mechanism of C-type oxidases are discussed.

Variability of chlorophyll-a concentration in the Gulf of Guinea and its relation to physical oceanographic variables.

The Gulf of Guinea represents a wide tract of the African coast with complex and rich coastal ecosystems undergoing various pressures. The seasonal variations of chlorophyll-a concentration (Chla) along the Gulf of Guinea (GoG) and their relations with physical oceanographic variables were analyzed using satellite observations covering the period 2002-2012. The effects of sea surface temperature (SST), sea level anomalies (SLA), winds, geostrophic currents, eddy kinetic energy (EKE), mesoscale eddies and fronts were considered on a monthly time scale. The analysis for each unit area was carried out on a chlorophyll index (IChla) computed as the product of the mean distance from the coast to the eutrophic threshold (1 mg m-3 isoline) and the average Chla in the eutrophic area. The study, based on satellite-derived Chla, was allowed by the unprecedented coverage given by the products distributed by the ESA Ocean Colour Climate Change Initiative (OC_CCI) resulting from the merging of data from several satellite missions. The physical variables served as potential predictors in a statistical Boosted Regression Tree (BRT) model. To account for the heterogeneous nature of the GoG, the analysis was conducted on eight systems that made up a partition of the whole region defined on the basis of the BRT model results and climatological properties. The western-most domain, from Guinea-Bissau to Sierra Leone, was associated with upwelling properties in boreal winter and appeared to share some characteristics with the overall Northwest African upwelling system. The region of Ivory Coast and Ghana also had upwelling properties but the main upwelling season was in boreal summer. In general upwelling conditions with cold SST, negative SLA, fairly strong frontal activity, and moderate winds, appeared as the environmental window most favorable to high IChla values. For these systems, the BRT model fitted the IChla data well with a percentage of explained total deviance [Formula: see text] between 70% and 91% when using only physical oceanographic variables. Finally, the systems associated with the coasts of Nigeria to Gabon showed some mixed properties, with [Formula: see text] values of 54-60%. Among these systems, a common feature seemed to be the importance of river discharge to explain IChla variations. Where possible (for the Niger River in the Nigeria system), the addition of river data as predictor in the BRT model resulted in a significant increase of [Formula: see text] to 75%. Further progress is needed to understand the observed relationships and to predict how they can evolve in the face of climate change.

An evaluation of marine regions relevant for ocean color system vicarious calibration.

System Vicarious Calibration (SVC) is the fundamental process commonly implemented to meet uncertainty requirements in satellite ocean color data. It is performed by applying gain factors, g-factors, to the pre-launch calibration coefficients of the space sensor already corrected for sensitivity decay with time. Mission specific g-factors are determined from top-of-the-atmosphere data computed by propagating highly accurate in situ values of the water-leaving radiance, Lw, to the satellite sensor. Values of Lw from marine regions characterized by oligotrophic/mesotrophic waters and maritime aerosols, high environmental stability and spatial homogeneity, low cloudiness and absence of any source of land contamination, are essential to determine g-factors applicable to the creation of Climate Data Records (CDRs) from multiple ocean color missions. Accounting for the location of existing and potential new SVC fixed sites, marine regions satisfying SVC requirements for the generation of CDRs have been identified through the analysis of satellite data from recent ocean color missions.

Band shifting for ocean color multi-spectral reflectance data.

An approach to perform band shifting applied to multi-spectral ocean remote sensing reflectance RRS values in the visible spectral range is presented. The band-shifting scheme aims at expressing RRS at a wavelength not originally part of the spectrum from data at neighboring bands. The scheme relies on the determination of inherent optical properties (IOPs) by a bio-optical model, the calculation of the IOPs at the target wavelength using the spectral shapes assumed for each IOP, and the operation of the bio-optical model in forward mode to express RRS at the target wavelength. The performance of the band-shifting scheme applied to bands typical of satellite missions is assessed with hyper-spectral data sets obtained from radiative transfer simulations or from field measurements. The relative error ε on the conversion factors from 488 to 490 nm is mostly within 1%. Analogous results are obtained for conversions in the red spectral domain (665, 667 and 670 nm) only for synthetic data sets. The range of ε for conversions between green bands (547, 555 and 560 nm) is within 2% to 5% depending on the data set considered. Similar results are obtained when RRS values are computed at 510 nm from data at 488 and 531 nm. In the case of the assessment with simulated data, all band-shifting operations are characterized by an ε range within 2% for all conversions when the concentration of chlorophyll-a is lower than 1 mg m(-3). Applied to satellite data, the band-shifting scheme noticeably improves the agreement between RRS data from different missions.

Evidence for distinct electron transfer processes in terminal oxidases from different origin by means of protein film voltammetry.

Cytochrome aa3 from Paracoccus denitrificans and cytochrome ba3 from Thermus thermophilus, two distinct members of the heme-copper oxidase superfamily, were immobilized on electrodes modified with gold nanoparticles. This procedure allowed us to achieve direct electron transfer between the enzyme and the gold nanoparticles and to obtain evidence for different electrocatalytic properties of the two enzymes. The pH dependence and thermostability reveal that the enzymes are highly adapted to their native environments. These results suggest that evolution resulted in different solutions to the common problem of electron transfer to oxygen.

Investigating the thermostability of succinate: quinone oxidoreductase enzymes by direct electrochemistry at SWNTs-modified electrodes and FTIR spectroscopy.

Succinate: quinone reductases (SQRs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. Herein, we compare the temperature-dependent activity and structural stability of two SQRs, the first from the mesophilic bacterium Escherichia coli and the second from the thermophilic bacterium Thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. Direct electron transfer was achieved with full membrane protein complexes at single-walled carbon nanotube (SWNT)-modified electrodes. The possible structural factors that contribute to the temperature-dependent activity of the enzymes and, in particular, to the thermostability of the Thermus thermophilus SQR are discussed.

The marine diversity spectrum.

Distributions of species body sizes within a taxonomic group, for example, mammals, are widely studied and important because they help illuminate the evolutionary processes that produced these distributions. Distributions of the sizes of species within an assemblage delineated by geography instead of taxonomy (all the species in a region regardless of clade) are much less studied but are equally important and will illuminate a different set of ecological and evolutionary processes. We develop and test a mechanistic model of how diversity varies with body mass in marine ecosystems. The model predicts the form of the 'diversity spectrum', which quantifies the distribution of species' asymptotic body masses, is a species analogue of the classic size spectrum of individuals, and which we have found to be a new and widely applicable description of diversity patterns. The marine diversity spectrum is predicted to be approximately linear across an asymptotic mass range spanning seven orders of magnitude. Slope -0.5 is predicted for the global marine diversity spectrum for all combined pelagic zones of continental shelf seas, and slopes for large regions are predicted to lie between -0.5 and -0.1. Slopes of -0.5 and -0.1 represent markedly different communities: a slope of -0.5 depicts a 10-fold reduction in diversity for every 100-fold increase in asymptotic mass; a slope of -0.1 depicts a 1.6-fold reduction. Steeper slopes are predicted for larger or colder regions, meaning fewer large species per small species for such regions. Predictions were largely validated by a global empirical analysis. Results explain for the first time a new and widespread phenomenon of biodiversity. Results have implications for estimating numbers of species of small asymptotic mass, where taxonomic inventories are far from complete. Results show that the relationship between diversity and body mass can be explained from the dependence of predation behaviour, dispersal, and life history on body mass, and a neutral assumption about speciation and extinction.

Quest for a stable Cu-ligand complex with a high catalytic activity to produce reactive oxygen species.

Metal ion-catalyzed overproduction of reactive oxygen species (ROS) is believed to contribute significantly to oxidative stress and be involved in several biological processes, from immune defense to development of diseases. Among the essential metal ions, copper is one of the most efficient catalysts in ROS production in the presence of O2 and a physiological reducing agent such as ascorbate. To control this chemistry, Cu ions are tightly coordinated to biomolecules. Free or loosely bound Cu ions are generally avoided to prevent their toxicity. In the present report, we aim to find stable Cu-ligand complexes (Cu-L) that can efficiently catalyze the production of ROS in the presence of ascorbate under aerobic conditions. Thermodynamic stability would be needed to avoid dissociation in the biological environment, and high ROS catalysis is of interest for applications as antimicrobial or anticancer agents. A series of Cu complexes with the well-known tripodal and tetradentate ligands containing a central amine linked to three pyridyl-alkyl arms of different lengths were investigated. Two of them with mixed arm length showed a higher catalytic activity in the oxidation of ascorbate and subsequent ROS production than Cu salts in buffer, which is an unprecedented result. Despite these high catalytic activities, no increased antimicrobial activity toward Escherichia coli or cytotoxicity against eukaryotic AGS cells in culture related to Cu-L-based ROS production could be observed. The potential reasons for discrepancy between in vitro and in cell data are discussed.

Recent advances in the electrochemistry and spectroelectrochemistry of membrane proteins.

Integral membrane proteins are encountered in fundamental natural processes, such as photosynthesis and respiration. The relation between the structure of the proteins and their function and dynamics are still not clear in most cases. Once fully understood, these processes could ultimately help researchers to develop alternative methods for producing energy, either from light or biomass. They could also lead to more efficient antibiotics, which would selectively inhibit a specific membrane protein of pathogenic bacteria. Since the chemical reactions involved in both photosynthesis and respiration are redox reactions, electrochemical methods can play a considerable role in uncovering their mechanisms. The electrochemical characterization of membrane proteins is, however, quite challenging. An overview on the techniques used for the characterization of membrane proteins, including classical approaches such as voltammetry and spectroelectrochemistry, and recent developments, such as their combination with surface-enhanced techniques is given.

Direct Electrochemistry of Cytochrome bo Oxidase at a series of Gold Nanoparticles-Modified Electrodes.

New membrane-protein based electrodes were prepared incorporating cytochrome bo(3) from E. coli and gold nanoparticles. Direct electron transfer between the electrode and the immobilized enzymes was achieved, resulting in an electrocatalytic activity in presence of O(2). The size of the gold nanoparticles was shown to be important and smaller particles were shown to reduce the overpotential of the process.

Generalized ocean color inversion model for retrieving marine inherent optical properties.

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensemble inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future emsemble applications.

Mutating the environment of heme b595 of E. coli cytochrome bd-I oxidase shifts its redox potential by 200 mV without inactivating the enzyme.

Cytochrome bd-I catalyzes the reduction of oxygen to water with the aid of hemes b558, b595 and d. Here, effects of a mutation of E445, a ligand of heme b595 and of R448, hydrogen bonded to E445 are studied electrochemically in the E. coli enzyme. The equilibrium potential of the three hemes are shifted by up to 200 mV in these mutants. Strikingly the E445D and the R448N mutants show a turnover of 41 ± 2 % and 20 ± 4 %, respectively. Electrocatalytic studies confirm that the mutants react with oxygen and bind and release NO. These results point towards the ability of cytochrome bd to react even if the electron transfer is less favorable.

pH-dependent kinetics of NO release from E. coli bd-I and bd-II oxidase reveals involvement of Asp/Glu58B.

Escherichia coli contains two cytochrome bd oxidases, bd-I and bd-II. The structure of both enzymes is highly similar, but they exhibit subtle differences such as the accessibility of the active site through a putative proton channel. Here, we demonstrate that the duroquinol:dioxygen oxidoreductase activity of bd-I increased with alkaline pH, whereas bd-II showed a broad activity maximum around pH 7. Likewise, the pH dependence of NO release from the reduced active site, an essential property of bd oxidases, differed between the two oxidases as detected by UV/vis spectroscopy. Both findings may be attributed to differences in the proton channel leading to the active site heme d. The channel comprises a titratable residue (Asp58B in bd-I and Glu58B in bd-II). Conservative mutations at this position drastically altered NO release demonstrating its contribution to the process.

E. coli cytochrome bd-I requires Asp58 in the CydB subunit for catalytic activity.

The reduction of oxygen to water is crucial to life and a central metabolic process. To fulfil this task, prokaryotes use among other enzymes cytochrome bd oxidases (Cyt bds) that also play an important role in bacterial virulence and antibiotic resistance. To fight microbial infections by pathogens, an in-depth understanding of the enzyme mechanism is required. Here, we combine bioinformatics, mutagenesis, enzyme kinetics and FTIR spectroscopy to demonstrate that proton delivery to the active site contributes to the rate limiting steps in Cyt bd-I and involves Asp58 of subunit CydB. Our findings reveal a previously unknown catalytic function of subunit CydB in the reaction of Cyt bd-I.

Ensemble uncertainty of inherent optical properties.

We present a method to evaluate the combined accuracy of ocean color models and the parameterizations of inherent optical proprieties (IOPs), or model-parametrization setup. The method estimates the ensemble (collective) uncertainty of derived IOPs relative to the radiometric error and is directly applicable to ocean color products without the need for inversion. Validation shows a very good fit between derived and known values for synthetic data, with R(2) > 0.95 and mean absolute difference (MADi) <0.25 m(-1). Due to the influence of observation errors, these values deteriorate to 0.45 < R(2) < 0.5 and 0.65 < MADi < 0.9 for in-situ and ocean color matchup data. The method is also used to estimate the maximum accuracy that could be achieved by a specific model-parametrization setup, which represents the optimum accuracy that should be targeted when deriving IOPs. Application to time series of ocean color global products collected between 1997-2007 shows few areas with increasing annual trends of ensemble uncertainty, up to 8 sr m(-1) decade(-1). This value is translated to an error of 0.04 m(-1) decade(-1) in the sum of derived absorption and backscattering coefficients at the blue wavelength 440 nm. As such, the developed method can be used as a tool for assessing the reliability of model-parametrization setups for specific biophysical conditions and for identifying hot-spots for which the model-parametrization setup should be reconsidered.