Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.

Synechocystis sp. PCC 6803 is the most popular cyanobacterial strain, serving as a standard in the research fields of photosynthesis, stress response, metabolism and so on. A glucose-tolerant (GT) derivative of this strain was used for genome sequencing at Kazusa DNA Research Institute in 1996, which established a hallmark in the study of cyanobacteria. However, apparent differences in sequences deviating from the database have been noticed among different strain stocks. For this reason, we analysed the genomic sequence of another GT strain (GT-S) by 454 and partial Sanger sequencing. We found 22 putative single nucleotide polymorphisms (SNPs) in comparison to the published sequence of the Kazusa strain. However, Sanger sequencing of 36 direct PCR products of the Kazusa strains stored in small aliquots resulted in their identity with the GT-S sequence at 21 of the 22 sites, excluding the possibility of their being SNPs. In addition, we were able to combine five split open reading frames present in the database sequence, and to remove the C-terminus of an ORF. Aside from these, two of the Insertion Sequence elements were not present in the GT-S strain. We have thus become able to provide an accurate genomic sequence of Synechocystis sp. PCC 6803 for future studies on this important cyanobacterial strain.

Brønsted and Lewis base catalysis of hexametalate clusters of group 5 metals [M­(V)6O19]8– (M­(V) = Ta, Nb) and group 6 metals [M­(VI)6O19]2– (M­(VI) = Mo, W) was studied using Knoevenagel condensation and CO2 fixation reaction, respectively, as test reactions. It was found from mass spectrometry and elemental analysis that tetrabutylammonium salts of [M­(V)6O19]8– were partially protonated to form [H4M­(V)6O19]4– under ambient conditions, whereas those of [M­(VI)6O19]2– were not. Base catalytic activity increased in the order of [Mo6O19]2–, [W6O19]2– ≪ [H4Nb6O19]4– < [H4Ta6O19]4–, which is consistent with the order of the average NBO charges on the surface O atoms. This trend suggests that the highest activity of [H4Ta6O19]4– is due to the large amount of negative charges on surface O atoms. Theoretical calculations on [H n Ta6O19](8–n)– (n = 1–4) demonstrated that protonation of the O atoms at the edges is energetically favorable regardless of n and that the NBO charges on the remaining unprotonated O atoms in [H4Ta6O19]4– are still more negative than those of pristine [Nb6O19]8–, [W6O19]2–, and [Mo6O19]2–. Theoretical calculations also predicted that CO2 can be reductively activated at all of the surface O atoms of [H4Ta6O19]4– regardless of their locations. This work demonstrates that group 5 polyoxometalates are promising candidates for active base catalysts.

The filamentous cyanobacterium Anabaena sp. PCC 7120 fixes dinitrogen facultatively. Upon depletion of combined nitrogen, about 10% of vegetative cells within the filaments differentiate terminally into nitrogen-fixing cells. The heterocyst has been studied as a model system of prokaryotic cell differentiation, with major focus on signal transduction and pattern formation. The fate of heterocyst differentiation is determined at about the eighth hour of induction (point of no return), well before conspicuous morphological or metabolic changes occur. However, little is known about how the initial heterocysts are selected after the induction by nitrogen deprivation. To address this question, we followed the fate of every cells on agar plates after nitrogen deprivation with an interval of 4 h. About 10% of heterocysts were formed without prior division after the start of nitrogen deprivation. The intensity of fluorescence of GFP in the transformants of hetR-gfp increased markedly in the future heterocysts at the fourth hour with respect to other cells. We also noted that the growing filaments consisted of clusters of four consecutive cells that we call quartets. About 75% of initial heterocysts originated from either of the two outer cells of quartets at the start of nitrogen deprivation. These results suggest that the future heterocysts are loosely selected at early times after the start of nitrogen deprivation, before the commitment. Such early candidacy could be explained by different properties of the outer and inner cells of a quartet, but the molecular nature of candidacy remains to be uncovered.

No abstract

No abstract

In steel refining process, an increase of interfacial area between the metal and slag through the metal droplets emulsified into the slag, so-called "metal emulsion", is one prevailing view for improving the reaction rate. The formation of metal emulsion was experimentally evaluated using Al-Cu alloy as metal phase and chloride salt as slag phase under the bottom bubbling condition. Samples were collected from the center of the salt phase in the container. Large number of metal droplets were separated from the salt by dissolving it into water. The number, surface area, and weight of the droplets increased with the gas flow rate and have local maximum values. The formation and sedimentation rates of metal droplets were estimated using a mathematical model. The formation rate increased with the gas flow rate and has a local maximum value as a function of gas flow rate, while the sedimentation rate is independent of the gas flow rate under the bottom bubbling condition. Three types of formation mode of metal emulsion, which occurred by the rupture of metal film around the bubble, were observed using high speed camera. During the process, an elongated column covered with metal film was observed with the increasing gas flow rate. This elongated column sometimes reached to the top surface of the salt phase. In this case, it is considered that fine droplets were not formed and in consequence, the weight of metal emulsion decreased at higher gas flow rate.KEY WORDS: metal emulsion; interfacial area; steelmaking; formation rate; sedimentation rate; formation mechanism of metal droplet.

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Proteins (COG). CyanoClust is a database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/.