Identification and characterization of d-arabinose reductase and d-arabinose transporters from Pichia stipitis

d-xylose and l-arabinose are the major constituents of plant lignocelluloses, and the related fungal metabolic pathways have been extensively examined. Although Pichia stipitis CBS 6054 grows using d-arabinose as the sole carbon source, the hypothetical pathway has not yet been clarified at the molecular level. We herein purified NAD(P)H-dependent d-arabinose reductase from cells grown on d-arabinose, and found that the enzyme was identical to the known d-xylose reductase (XR). The enzyme activity of XR with d-arabinose was previously reported to be only 1% that with d-xylose. The k_cat/K_m value with d-arabinose (1.27 min^?1 mM^?1), which was determined using the recombinant enzyme, was 13.6- and 10.5-fold lower than those with l-arabinose and d-xylose, respectively. Among the 34 putative sugar transporters from P. stipitis, only seven genes exhibited uptake ability not only for d-arabinose, but also for d-glucose and other pentose sugars including d-xylose and l-arabinose in Saccharomyces cerevisiae.     

Stability of cytochromes c′ from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure

Extremophiles - The stability of dimeric cytochrome c′ from a thermophile, as compared with that of a homologous mesophilic counterpart, is attributed to strengthened interactions around the...     

EcoBalance 2018—Nexus of ideas: innovation by linking through life cycle thinking (9–12 October 2018, Tokyo,Japan)

The International Journal of Life Cycle Assessment -     

Targeted exome sequencing of unselected heavy‐ion beam‐irradiated populations reveals less‐biased mutation characteristics in the rice genome

Heavy‐ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost‐efficient whole‐exome sequencing procedure in rice, and its application to characterize an unselected population of heavy‐ion beam‐induced mutations. The bioinformatics pipeline identified single‐nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy‐ion beams at the population level. In total, 165 individual M₂ lines derived from six irradiation conditions as well as eight pools from non‐irradiated ‘Nipponbare’ controls were sequenced using the newly established target exome sequencing procedure. The characteristics and distribution of carbon‐ion beam‐induced mutations were analyzed in the absence of bias introduced by visual mutant selections. The average (±SE) number of mutations within the target exon regions was 9.06 ± 0.37 induced by 150 Gy irradiation of dry seeds. The mutation frequency changed in parallel to the irradiation dose when dry seeds were irradiated. The total number of mutations detected by sequencing unselected M₂ lines was correlated with the conventional mutation frequency determined by the occurrence of morphological mutants. Therefore, mutation frequency may be a good indicator for sequencing‐based determination of the optimal irradiation condition for induction of mutations.     

Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface

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Molecular discrimination and phylogeographic patterns of clones of the parthenogenetic gecko Lepidodactylus lugubris in the Japanese Archipelago

Vertebrates usually reproduce sexually in which males and females contribute their offspring genome and produce genetically diverse offspring. However, some of them are asexual without genetic contribution from males. The nocturnal gecko, Lepidodactylus lugubris, is all females and reproduces parthenogenetically. This gecko is known to consist of diploid and triploid clones in the tropical and subtropical regions, which can be identified by their dorsal marking patterns, ploidy, and protein polymorphism. This gecko is also distributed in the southern parts of Japan, and several clones have been reported. In this study, we investigated the origins and genetic diversity of Japanese L. lugubris by clonal discrimination using microsatellite and mitochondrial DNA analyses. A total of 748 individuals were collected from 21 islands of five island groups (Ogasawara, Okinawa, Miyako, Yaeyama and Daito Islands) and 17 clones were distinguished genetically. Mitochondrial cyt b sequences of these clones suggested that they were all closely related and differentiated recently. Clonal diversity was much higher (14 clones) in the Daito Islands than in the other island groups in which only one or two clones coexisted. Judging from the dorsal marking patterns and ploidy known so far, six clones were cosmopolitan and may be colonized from the outside of Japan. However, other 11 clones were endemic to the Daito Islands and explained by possible hybridization between the one female diploid clone and one male diploid clone because other 9 clones were triploid and all had the combinations of polymorphic microsatellite alleles of these female and male diploid clones. Although the males have never been recorded in the Daito Islands, males might appear in the past. These findings contribute to understanding of clonal diversity and dynamics of asexually reproducing animals. If diploid parthenogenetic geckos can produce triploid clones by mating with the diploid males, clonal diversity would increase rapidly in a small island, and such newly produced triploid clones would expand widely.