Layout and results from the initial operation of the high-resolution x-ray imaging crystal spectrometer on the Large Helical Device.

First results of ion and electron temperature profile measurements from the x-ray imaging crystal spectrometer (XICS) diagnostic on the Large Helical Device (LHD) are presented. This diagnostic system has been operational since the beginning of the 2011 LHD experimental campaign and is the first application of the XICS diagnostic technique to helical plasma geometry. The XICS diagnostic provides measurements of ion and electron temperature profiles in LHD with a spatial resolution of 2 cm and a maximum time resolution of 5 ms (typically 20 ms). Ion temperature profiles from the XICS diagnostic are possible under conditions where charge exchange recombination spectroscopy (CXRS) is not possible (high density) or is perturbative to the plasma (low density or radio frequency heated plasmas). Measurements are made by using a spherically bent crystal to provide a spectrally resolved 1D image of the plasma from line integrated emission of helium-like Ar(16 +). The final hardware design and configuration are detailed along with the calibration procedures. Line-integrated ion and electron temperature measurements are presented, and the measurement accuracy is discussed. Finally central temperature measurements from the XICS system are compared to measurements from the Thomson scattering and CXRS systems, showing excellent agreement.

Objectives and layout of a high-resolution x-ray imaging crystal spectrometer for the large helical device.

A high-resolution x-ray imaging crystal spectrometer, whose concept was tested on NSTX and Alcator C-Mod, is being designed for the large helical device (LHD). This instrument will record spatially resolved spectra of helium-like Ar(16+) and will provide ion temperature profiles with spatial and temporal resolutions of <2 cm and ≥10 ms, respectively. The spectrometer layout and instrumental features are largely determined by the magnetic field structure of LHD. The stellarator equilibrium reconstruction codes, STELLOPT and PIES, will be used for the tomographic inversion of the spectral data.

Eliminating islands in high-pressure free-boundary stellarator magnetohydrodynamic equilibrium solutions.

Magnetic islands in free-boundary stellarator equilibria are suppressed using a procedure that iterates the plasma equilibrium equations and, at each iteration, adjusts the coil geometry to cancel resonant fields produced by the plasma. The coils are constrained to satisfy certain measures of engineering acceptability and the plasma is constrained to ensure kink stability. As the iterations continue, the coil geometry and the plasma simultaneously converge to an equilibrium in which the island content is negligible. The method is applied with success to a candidate plasma and coil design for the National Compact Stellarator Experiment [Phys. Plasmas 8, 2083 (2001)]].

DNA shuffling method for generating highly recombined genes and evolved enzymes.

We introduce a method of in vitro recombination or "DNA shuffling" to generate libraries of evolved enzymes. The approach relies on the ordering, trimming, and joining of randomly cleaved parental DNA fragments annealed to a transient polynucleotide scaffold. We generated chimeric libraries averaging 14.0 crossovers per gene, a several-fold higher level of recombination than observed for other methods. We also observed an unprecedented four crossovers per gene in regions of 10 or fewer bases of sequence identity. These properties allow generation of chimeras unavailable by other methods. We detected no unshuffled parental clones or duplicated "sibling" chimeras, and relatively few inactive clones. We demonstrated the method by molecular breeding of a monooxygenase for increased rate and extent of biodesulfurization on complex substrates, as well as for 20-fold faster conversion of a nonnatural substrate. This method represents a conceptually distinct and improved alternative to sexual PCR for gene family shuffling.

Biodesulfurization and the upgrading of petroleum distillates.

Biotechnology offers an alternative way to process fossil fuels. There have been several important advances in the elucidation of the mechanisms of biodesulfurization and the development of a biocatalytic desulfurization process. These include a detailed analysis of the rate and extent of desulfurization of real target molecules in a diesel matrix, the directed evolution of rate- and extent-limiting enzymes for better performance and the expression of the genes in alternative hosts. Process innovations include new reactor designs, separations and recovery strategies and the production of value-added byproducts during desulfurization.

A flavin reductase stimulates DszA and DszC proteins of Rhodococcus erythropolis IGTS8 in vitro.

Rhodococcus erythropolis IGTS8 is a gram positive bacterium, which can catabolize dibenzothiophene to 2-hydroxybiphenyl and inorganic sulfur without the cleavage of carbon-carbon bonds. Three structural genes, dszA, dszB, and dszC, have been cloned and shown to be necessary for this phenotype. Here, we demonstrate that a FMN:NADPH oxidoreductase from Vibrio harveyi complements activities of purified DszA and DszC proteins. Furthermore, we propose that DszA and DszC are oxygenase units that do not use NAD(P)H directly, but instead use FMNH2 from a FMN:NADPH oxidoreductase for oxygenation.

Molecular mechanisms of biocatalytic desulfurization of fossil fuels.

The development of biocatalytic desulfurization of petroleum fractions may allow its use in place of conventional hydrodesulfurization (HDS). Dibenzothiophene (DBT) is representative of a broad range of sulfur heterocycles found in petroleum that are recalcitrant to desulfurization via HDS. Rhodococcus sp. strain IGTS8 has the ability to convert DBT to 2-hydroxybiphenyl (HBP) with the release of inorganic sulfur. The conversion of DBT to HBP is catalyzed by a multienzyme pathway consisting of two monooxygenases and a desulfinase. The final reaction catalyzed by the desulfinase appears to be the rate limiting step in the pathway. Each of the enzymes has been purified to homogeneity and their kinetic and physical properties studied. Neither monooxygenase has a tightly bound cofactor and each requires an NADH-FMN oxidoreductase for activity. An NADH-FMN oxidoreductase has been purified from Rhodococcus and is a protein of approximately 25,000 molecular weight with no apparent sequence homology to any other protein in the databases. We describe a unique sulfur acquisition system that Rhodococcus uses to obtain sulfur from very stable heterocyclic molecules.

Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8.

The dsz gene cluster of Rhodococcus erythropolis IGTS8 comprises three genes, dszA, dszB, and dszC, whose products are involved in the conversion of dibenzothiophene (DBT) to 2-hydroxybiphenyl and sulfite. This organism can use DBT as the sole sulfur source but not as a carbon source. Dsz activity is repressed by methionine, cysteine, Casamino Acids, and sulfate but not by DBT or dimethyl sulfoxide. We cloned 385 bp of the DNA immediately 5' to dszA in front of the reporter gene lacZ of Escherichia coli. We showed that this region contains a Rhodococcus promoter and at least three dsz regulatory regions. After hydrazine mutagenesis of this DNA, colonies that were able to express beta-galactosidase in the presence of Casamino Acids were isolated. Sequencing of these mutants revealed two possible regulatory regions. One is at -263 to -244, and the other is at -93 to -38, where -1 is the base preceding the A of the initiation codon ATG of dszA. An S1 nuclease protection assay showed that the start of the dsz promoter is the G at -46 and that transcription is repressed by sulfate and cysteine but not by dimethyl sulfoxide. The promoter encompasses a region of potential diad symmetry that may contain an operator. Immediately upstream of the promoter is a protein-binding domain between -146 and -121. Deletion of this region did not affect repression, but promoter activity appeared to be reduced by threefold. Thus, it could be an activator binding site or an enhancer region.

Plasmid-borne Tn5 insertion mutation resulting in accumulation of gentisate from salicylate.

Plasmid-borne Tn5 insertion mutants of a Pseudomonas species which accumulated 2,5-dihydroxybenzoate (gentisate) following growth on 2-hydroxybenzoate (salicylate) were obtained from a pool of mutants that were unable to grow on naphthalene. One such mutant was characterized further. The ability of this mutant to oxidize gentisate was 100-fold less than the ability of a Nah+ Sal+ strain harboring the unmutagenized plasmid, although both strains oxidized and grew on salicylate. These bacteria were presumably able to metabolize salicylate via catechol, since they possessed an inducible, plasmid-encoded catechol 2,3-dioxygenase. Our results suggest that there is an alternate, plasmid-encoded route of salicylate degradation via gentisate and that some plasmid-associated relationship between this pathway and naphthalene oxidation exists.

Plasmid-mediated degradation of dibenzothiophene by Pseudomonas species.

The microbial transformation of dibenzothiophene (DBT) is of interest in the potential desulfurization of oil. We isolated three soil Pseudomonas species which oxidized DBT to characteristic water-soluble, sulfur-containing products. Two of our isolates harbored a 55-megadalton plasmid; growth in the presence of novobiocin resulted in both loss of the plasmid and loss of the ability to oxidize DBT. Reintroduction of the plasmid restored the ability to oxidize DBT to water-soluble products. The products resulting from the oxidation of DBT were characterized and included 3-hydroxy-2-formyl benzothiophene, 3-oxo-[3'-hydroxy-thionaphthenyl-(2)-methylene]-dihydrothionaph thene, and the hemiacetal and trans forms of 4-[2-(3-hydroxy)-thianaphthenyl]-2-oxo-3-butenoic acid. The products of DBT oxidation were inhibitory to cell growth and further DBT oxidation. DBT oxidation in our soil isolates was induced by naphthalene or salicylate and to a much lesser extent by DBT and was repressed by succinate.

Isoleucine synthesis by Clostridium sporogenes from propionate or alpha-methylbutyrate.

Preliminary studies demonstrated that Clostridium sporogenes synthesized isoleucine by a pathway not involving threonine or threonine dehydratase. Radiotracer experiments with cells grown in a defined carbohydrate-free medium showed that radioactivity from [U-14C]serine, [3-14C]pyruvate, [14C]NaHCO3 and [1-], [2-] and [3-14C]propionate was incorporated into isoleucine. Conversely, there was no detectable incorporation of 14C into isoleucine during growth with [U-14C]glutamate, [U-14C]threonine, [U-14C]valine, [U-14C]leucine or [U-14C]methionine. Crude extracts of the bacteria grown in a minimal medium contained levels of alpha-acetohydroxyacid synthase activities comparable to those in Escherichia coli K12 grown in minimal medium. Stepwise degradation of isoleucine obtained from C. sporogenes grown in the presence of specifically-labelled precursors indicated that C. sporogenes can make isoleucine via the reductive carboxylation of propionate to yield alpha-oxobutyrate, which is metabolized to isoleucine in the classical fashion. Isoleucine was also formed by C. sporogenes via the reductive carboxylation of alpha-methylbutyrate to alpha-oxo-beta-methylvalerate.

Interconversion of valine and leucine by Clostridium sporogenes.

Clostridium sporogenes has been found to require L-leucine and L-valine for growth in a minimal medium, although valine can be replaced by isobutyrate and leucine by isovalerate. Cells grown in minimal media incorporated significant 14C from [14C]valine into leucine and from [14C]leucine into valine. Growth with [4,5-3H]leucine also resulted in the incorporation of 3H into valine. These results indicate that these bacteria can interconvert leucine and valine.

Purification and partial characterization of proline dehydrogenase from Clostridium sporogenes.

A proline dehydrogenase which catalyzes the nicotinamide adenine dinucleotide (NAD) dependent oxidation of proline and the NADH-dependent reduction of delta 1-pyrroline 5-carboxylic acid (PCA) was purified from extracts of Clostridium sporogenes. Following purification, only one protein band was found on analytical polyacrylamide disc gels and on sodium dodecyl sulfate (SDS) - polyacrylamide disc gels. Sucrose density gradient centrifugation and SDS-gel electrophoresis indicated that the enzyme has a molecular weight of approximately 217 000 and consists of two subunits of equal size. During purification of proline dehydrogenase on hydroxylapatite the ratio of dehydrogenase activity to reductase activity decreases significantly, and a similar change in ratio was brought about by storage of partially purified enzyme preparations in low ionic strength buffers. Subsequent purification did not change the ratio. The dehydrogenase activity of proline dehydrogenase was inhibited by L-glutamate (Ki = 0.32 mM at pH 7.4 and Ki = 0.65 mM at ph 10.2). However, the reductase activity of the purified enzyme was not affected by 100 mM L-glutamate.