43 research outputs found
Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics
BACKGROUND: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. METHODOLOGY/PRINCIPAL FINDINGS: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. CONCLUSIONS/SIGNIFICANCE: Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification
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Design of a harmonic generation FEL experiment at BNL
We present design parameters of a harmonic generation FEL experiment to be carried out at the Accelerator Test Facility (ATF) at BNL. This experiment out as a proof-of-principle for the proposed UV-FEL User's Facility at BNL. In the experiment we plan to triple the frequency of a CO{sub 2} seed laser by utilizing two superconducting wigglers and a dispersive section. The first wiggler will be used in conjunction with the CO{sub 2} seed laser to generate a ponderomotive force that will bunch the electron beam. The bunching will then be enhanced by the dispersion section. The second wiggler, tuned to the third harmonic of the seed laser will follow. In the beginning of the second wiggler the bunched beam will produce super-radiant emission (characterized by a quadratic growth of the radiated power), then the radiation will be amplified exponentially. The last part of the wiggler will be tapered. We plan to study the evolution of the various radiation growth mechanisms as well as the coherence of the tripled and exponentially amplified radiation. 12 refs
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A superconducting short period undulator for a harmonic generation FEL experiment
A three stage superconducting (SC) undulator for a high gain harmonic generation (HGE) FEL experiment in the infrared is under construction at the NSLS in collaboration with Grumman Corporation. A novel undulator technology suitable for short period (6--40mm) undulators will be employed for all three stages, the modulator, the dispersive section and the radiator. The undulator triples the frequency of a 10.4[mu]m CO[sub 2] seed laser. So far a 27 period (one third of the final radiator) prototype radiator has been designed, built and tested
The Phytoene synthase gene family of apple (Malus x domestica) and its role in controlling fruit carotenoid content
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