Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry

Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650 nm to 710 nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization

Imaging and modelling of poly(3-hydroxybutyrate) synthesis in Paracoccus denitrificans

Poly(3-hydroxybutyrate) (PHB) granule formation in Paracoccus denitrificans Pd1222 was investigated by laser scanning confocal microscopy (LSCM) and gas chromatography analysis. Cells that had been starved for 2 days were free of PHB granules but resynthesized them within 30 min of growth in fresh medium with succinate. In most cases, the granules were distributed randomly, although in some cases they appeared in a more organized pattern. The rates of growth and PHB accumulation were analyzed within the frame of a Genome-Scale Metabolic Model (GSMM) containing 781 metabolic genes, 1403 reactions and 1503 metabolites. The model was used to obtain quantitative predictions of biomass yields and PHB synthesis during aerobic growth on succinate as sole carbon and energy sources. The results revealed an initial fast stage of PHB accumulation, during which all of the acetyl-CoA originating from succinate was diverted to PHB production. The next stage was characterized by a tenfold lower PHB production rate and the simultaneous onset of exponential growth, during which acetyl-CoA was predominantly drained into the TCA cycle. Previous research has shown that PHB accumulation correlates with cytosolic acetyl-CoA concentration. It has also been shown that PHB accumulation is not transcriptionally regulated. Our results are consistent with the mentioned findings and suggest that, in absence of cell growth, most of the cellular acetyl-CoA is channeled to PHB synthesis, while during exponential growth, it is drained to the TCA cycle, causing a reduction of the cytosolic acetyl-CoA pool and a concomitant decrease of the synthesis of acetoacetyl-CoA (the precursor of PHB synthesis)

Biochemistry and Molecular Biology of Nitrification

The biochemistry and molecular biology of nitrification are poorly understood, almost certainly related to the difficult problem of growing large enough quantities of cells from which to prepare vesicular membranes and purified proteins. This chapter explains the biochemistry and molecular biology of nitrification. Nitrosomonas and Nitrobacter depend on a chemiosmotic mechanism of energy transduction. Many of the special biochemical features of Nitrosomonas and Nitrobacter need to be understood in the context of the ability of the electron transport system to catalyze reversed electron transfer. The demonstration of H_ pumping by intact cells fed with electrons from the nonphysiological donor ascorbate can be taken as support for the H_ pumping activity. The genome sequence clearly shows two reading frames, designated NorA and NorB on the basis of earlier partial sequence information. Bioenergetic arguments have suggested a location at the cytoplasmic surface, but immunolabeling studies have indicated the opposite. The oxidation of ammonia to NO2- by Nitrosomonas is not a straightforward process. The idea that ubiquinol provides electrons for the ammonia mono-oxygenase is supported by the fact that partially purified preparations of the enzyme can use duroquinol as electron donor

The Prokaryotic Nitrate Reductases

This chapter reviews the structural organization and bioenergetics of the four prokaryotic NO3 reductases and the eukaryotic enzyme and explores the possible mechanisms of NO3 transport. The membrane-bound NO3- reductase with the active site facing the cytoplasm is usually a three-subunit enzyme composed of NarGHI. The Mo ion of NarG is coordinated by an aspartate ligand provided by the polypeptide chain. Adjacent to the structural genes of NarGHI in many denitrifying bacteria are one or two members of genes encoding transport proteins generally known as NarK family proteins. Where respiratory NO3 reduction has been identified in Archaea, it is predicted to take place in a catalytic subunit with a twin arginine-dependent translocase (TAT) signal peptide, which may serve to export folded redox proteins across the cytoplasmic membrane. Periplasmic NO3 reductases (Nap) are also linked to quinol oxidation in respiratory electron transport chains but do not transduce the free energy in the QH2NO3 coupled into an H motive force. Bioinformatic analyses reveal that the Nap is phylogenetically widespread in proteobacteria, but detailed biochemical and spectroscopic studies have been restricted to enzymes from relatively few species. Some fungi have the capacity to reduce NO3 as part of a denitrification process and here the NO3 reductase is located in the mitochondrial membrane and is likely to emerge as being a prokaryotic pNar or nNar type

Introduction to the Biochemistry and Molecular Biology of Denitrification

This chapter provides an overview of the biochemistry and genetics of denitrification in such organisms. It considers the aspects of denitrification that occur in archaea and certain fungi. Denitrification has been mostly studied in Paracoccus denitrificans and Pseudomonas stutzeri and so it describes denitrification for each of these organisms in turn before considering to what extent general principles can be discerned. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO-reductase. In general, the proteins required for denitrification are only produced under (close to) anaerobic conditions, and if anaerobically grown, cells are exposed to O2 and then the activities of the proteins are inhibited. Specialized denitrifiers, such as P. denitrificans and the denitrifying Pseudomonads, contain more than 40 genes, which encode the proteins that make up a full denitrification pathway. They include the structural genes for the enzymes and e- donors, their regulators as well as many accessory genes required for assembly, cofactor synthesis, and insertion into the enzymes. In contrast, some denitrifiers can only carry out the two central reactions of the pathway and use these activities to support growth, but the cost of maintaining this capability is a very small amount of genome space. It provides insights into the regulation of gene expression and the way in which some denitrification enzymes play different roles in bacteria

Pseudoazurin mediates periplasmic electron flow in a mutant strain of Paracoccus denitrificans lacking c550.

AbstractA periplasmic protein able to transfer electrons from cytoplasmic membrane to the periplasmic nitrite reductase (cytochrome cd1) has been purified from the anoxically grown cytochrome c550 mutant strain Pd2121 and shown to be pseudoazurin by several independent criteria (molecular mass, copper content, visible spectrum, N-terminal amino acid sequence). Under our assay conditions, the half-saturation of electron transport occurred at about 10 μM pseudoazurin; the reaction was retarded by increasing ionic strength

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

Persistency of organic chemicals is a key property in their environmental risk assessment. Information on persistency is often derived from the results of biodegradability screening tests such as the ready biodegradability tests (RBTs). RBTs are, however, not designed for this purpose and suffer from several problems that lead to a high variability of the results and, hence, to difficulties in their interpretation. The origin and exposure history of the inocula used for biodegradability testing can lead to highly variable outcomes. Microbial adaptation to chemicals and its impact on biodegradation needs further investigation in order to have a better understanding of their effects on persistency assessments of chemicals. It is well described that microbial adaptation stimulates biodegradation of organic chemicals. Several mechanisms responsible for these phenomena have been described, amongst which are i) shifts in community composition or abundances, ii) mutations within populations, iii) horizontal gene transfer or iv) recombination events. These adaptation processes may well be mimicked under laboratory conditions, but the outcome remains difficult to predict as we lack a fundamental understanding of the adaptive responses. This review aims to bring together our current knowledge regarding microbial adaptation and its implication for the testing of biodegradation of chemicals

Stereoselective Chemoenzymatic Cascade Synthesis of the bis-THF Core of Acetogenins

bis-Tetrahydrofuran acetogenins are a class of natural products displaying highly potent and selective anti-tumor activity. Herein we report a new route to precursors of these natural products, utilizing the pseudo C2-symmetry in the central bis-tetrahydrofuran fragment. Key steps of our stereoselective chemoenzymatic strategy include the epoxide hydrolase-mediated desymmetrization of meso-epoxides and a cascade cyclization in either “inside-out” or “outside-in” direction, providing stereoselective access to the cores of both bullatacin- and rolliniastatin 1-type acetogenins with 6 stereocenters each from a common mono-epoxide precursor