Establishing the independent culture of a strictly symbiotic bacterium Symbiobacterium thermophilum from its supporting Bacillus strain.

Symbiobacterium thermophilum is a strictly symbiotic thermophile, the growth of which is dependent on the coexistence of an associating thermophilic Bacillus sp., strain S. S. thermophilum grows only in mixed culture with the Bacillus strain in liquid media, and does not form visible colonies on solid media. To measure the growth of this symbiotic bacterium and to analyze its growth requirements, we developed a quantitative PCR method by using its specific sequences in a putative membrane translocator gene tnaT as primers. According to this method, independent growth of S. thermophilum was first confirmed in a dialyzing culture physically separated from Bacillus strain S with a cellulose membrane. Independent growth of S. thermophilum was also managed by adding conditioned medium prepared from the culture filtrate of the Bacillus strain, but the growth in the conditioned medium stopped at a very limited extent with appearance of filamentous cells, suggesting the uncoupling of cellular growth and cell division. Formation of micro-colonies of S. thermophilum was observed on the conditioned agar medium under both aerobic and anaerobic conditions, but the colony-forming efficiencies remained below 1%. Several other bacterial species, such as Bacillus stearothermophilus, Bacillus subtilis, Thermus thermophilus, and even Escherichia coli, were also found to support the growth of S. thermophilum. These results indicate that S. thermophilum essentially requires some ubiquitous metabolite(s) of low molecular weight produced by various bacterial species as growth factor(s) but coexistence of the living partner cells is still required, probably to maintain an effective level of the putative factor(s) in the medium.     

DNA recognition by β-sheets

The modes of DNA recognition by β-sheets are analyzed by using the known crystal and solution three-dimensional structures of DNA-protein complexes. Close fitting of the protein surface and the DNA surface determines the binding geometry. Interaction takes place so that essentially the N-to-C direction of the β-strands either follows or crosses the DNA groove. Upon following the major groove a two-stranded antiparallel β-sheet dives into the groove and contacts DNA bases with its convex side facing the DNA, while upon following the minor groove, it binds around the sugar-phosphate backbones, with its opposite concave side shielding the DNA. In order for the β-strands crossing the minor groove to interact with the DNA, the dinucleotide steps need to almost totally helically untwist and roll around major groove. The β-sheet, on the other hand, needs to adopt a concave curvature on the binding surface in the direction that follows the DNA minor groove, and a convex surface in the direction that bridges the sugar-phosphate backbones across the groove. The result is to produce a hyperbolic paraboloidal DNA-binding surface. © 1998 John Wiley & Sons, Inc. Biopoly 44: 335–359, 1997     

Discovery and SAR of a novel series of Natriuretic Peptide Receptor-A (NPR-A) agonists

Novel thienopyrimidine compounds 2 and 3 were discovered from high-throughput screening as Natriuretic Peptide Receptor A (NPR-A) agonists. Scaffold hopping of a thienopyrimidine ring to a quinazoline ring, introduction of the basic functional group and optimization of the substituent on the 6-position of the benzene ring of quinazoline led to improved agonistic activity. We discovered compound 48, which showed potent agonistic activity for NPR-A with an EC₅₀ value of 0.073 μM, indicating 350-fold potency compared to the hit compound 3.     

Occurrence and reproduction of tropical fishes in ocean warming hotspots of Japanese temperate reefs

Reproduction of tropical species beyond their geographic range associated with ocean warming is regarded as the key indicator of a range shift. However, the lack of historical breeding records poses challenges for detecting distinct range shifts of tropical fishes. To obtain baseline data of the current status of the occurrence and breeding activity of tropical pomacentrid and apogonid fishes in ocean warming hotspots of temperate reefs (Kochi and Wakayama, 33°N) of Japan, we conducted a two-year underwater visual survey and synthesized those data with recently published information. By combining data from the present as well as past studies, the results confirmed the occurrence of 52 pomacentrid and 34 apogonid species, whereas breeding activity was confirmed for 19 and 16 species, respectively. Species richness and abundance of recruitment periphery and breeding active species were high at the warmer site adjacent to the Kuroshio Current. Most observed species were found beyond their known geographic range. Some species showing active breeding were widespread tropical fishes (e.g., Amphiprion clarkii, Pomacentrus coelestis and Apogon notatus) and probably have established breeding populations irrespective of recent global warming. The winter sea water temperature around the study sites will continue to rise, increasing by >2 °C by the end of the century; therefore, our results are highly relevant and represent the first step to elucidate the potential range extension of tropical fishes into temperate reefs with climate change.     

Pyramiding of male-sterile genes in <Emphasis Type="Italic">Cryptomeria japonica</Emphasis> D. Don with the aid of closely linked markers

Gene pyramiding is a breeding method used to combine multiple useful genes. Although several genes have been pyramided in certain crops, gene pyramiding has not previously been applied to forest trees. In this study, we used the markers closely linked to the two male-sterile genes MS1 and MS2 for the effective development of individuals doubly heterozygous for these two genes. This is the first example of gene pyramiding through marker-assisted selection (MAS) in forest trees. The markers gSNP06239, which is closely linked to the MS1 gene, and estSNP00695, which is closely linked to MS2, were used in MAS. On the basis of the linkage phase between the markers and male-sterile loci, we selected five F₁ individuals (S3-64 from Shindai-3 × Kamikiri-31, S3-70 from Shindai-3 × Kamikiri-38, S3-77 from Shindai-3 × Kamikiri-47, S1-22 from Shindai-1 × Nakakubiki-4, and S1-56 from Shindai-1 × Setsugai-20) as parents for artificial crossing. The 268 seedlings obtained from six artificial cross combinations were used in this study. Chi-squared tests showed no significant deviation from the expected Mendelian ratios of genotypes, indicating that MAS using markers closely linked to the male-sterile genes worked very well. Fifteen individuals that showed unexpected genotypes were probably recombinants, because the map distances between the male-sterile locus and the DNA markers were 4.1 cM (gSNP06239 to MS1) and 6.9 cM (estSNP00695 to MS2). Development of markers more closely linked to the male-sterile loci will facilitate precise gene pyramiding in the future.     

Geographic patterns of genetic variation in nuclear and chloroplast genomes of two related oaks (<Emphasis Type="Italic">Quercus aliena</Emphasis> and <Emphasis Type="Italic">Q. serrata</Emphasis>) in Japan: implications for seed and seedling transfer

In this study, we assessed geographic patterns of genetic variations in nuclear and chloroplast genomes of two related native oaks in Japan, Quercus aliena and Q. serrata, in order to facilitate development of genetic guidelines for transfer of planting stocks for each species. A total of 12 populations of Q. aliena and 44 populations of Q. serrata were analyzed in this study. Genotyping of nuclear microsatellites in Q. aliena was done with only nine populations (n = 212) due to limited numbers of individuals in two populations, while all 12 populations (n = 89) were used in sequencing chloroplast DNA (cpDNA). In Q. serrata, 43 populations (n = 1032) were genotyped by nuclear microsatellite markers, while cpDNA of 44 populations (n = 350) was sequenced. As anticipated, geographic patterns detected in the variations of Q. aliena’s nuclear genome and its chloroplast haplotype distribution clearly distinguished northern and southern groups of populations. However, those of Q. serrata were inconsistent. The geographic distribution of its chloroplast haplotypes tends to show the predicted differentiation between northern and southern lineages, but geographic signals in the genetic structure of its nuclear microsatellites are weak. Therefore, treating northern and southern regions of Japan as genetically distinct transferrable zones for planting stocks is highly warranted for Q. aliena. For Q. serrata, the strong NE-SW geographic structure of cpDNA should be considered.     

Purification processes, ecological functions, planning and design of riparian buffer zones in agricultural watersheds

Two international meetings on ecological engineering, with a focus on riparian buffer zones, served as the source for selected papers in this special issue: (1) an International Workshop on Efficiency of Purification Processes in Riparian Buffer Zones: Their Design and Planning in Agricultural Watersheds, jointly organised by Hokkaido University, Japan, the National Agricultural Research Center for Hokkaido Region, Japan, Civil Engineering Research Institute of Hokkaido, Japan, and the Institute of Geography, University of Tartu, Estonia, and held from 5 to 9 November 2001 in Kushiro City, Hokkaido, Japan; and (2) an International Conference on Ecological Engineering for Landscape Services and Products, jointly organised by the International Ecological Engineering Society (IEES) and Lincoln University, Christchurch, New Zealand, and held from 25 to 29 November 2001 in Christchurch, New Zealand. At these two meetings, altogether 94 oral presentations (17 from invited speakers) and 15 posters by representatives from 21 countries were presented. The editorial paper highlights trends in investigation of the purification processes in riparian buffer zones as well as planning, design and management aspects of riparian buffers regarding the wide spectrum of their ecological functions; it characterises the two international meetings which served as sources for the selected papers and briefly explains the main aspects of these papers.     

Characterization of novel alcohol dehydrogenase of Devosia riboflavina involved in stereoselective reduction of 3-pyrrolidinone derivatives

Optically active N-benzyl-3-pyrrolidinols are versatile chiral building blocks. Stereoselective reduction of N-benzyl-3-pyrrolidinone is an economical and environmentally friend means of synthesizing these compounds. Devosia riboflavina KNK10702 was discovered on screening as a source of a reducing enzyme giving the (R)-form N-benzyl-3-pyrrolidinol. An NADH-dependent alcohol dehydrogenase was purified to homogeneity through five steps from this microorganism. The relative molecular mass of the enzyme was estimated to be 58,000 on gel filtration and 28,000 on SDS-polyacrylamide gel electrophoresis. This enzyme reduced a broad range of carbonyl compounds in addition to N-substituted-3-pyrrolidinones. Some properties of the enzyme are reported herein.     

Novel families of vacuolar amino acid transporters

Amino acids are compartmentalized in the vacuoles of microorganisms and plants. In Saccharomyces cerevisiae, basic amino acids accumulate preferentially into vacuoles but acidic amino acids are almost excluded from them. This indicates that selective machineries operate at the vacuolar membrane. The members of the amino acid/auxin permease family and the major facilitator superfamily involved in the vacuolar compartmentalization of amino acids have been recently identified in studies using S. cerevisiae. Homologous genes for these transporters are also found in plant and mammalian genomes. The physiological significance in response to nitrogen starvation can now be discussed.