Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum

Thermoplasma acidophilum is a thermo-acidophilic archaeon. We purified tRNA^Leu (UAG) from T. acidophilum using a solid-phase DNA probe method and determined the RNA sequence after determining via nucleoside analysis and m⁷G-specific aniline cleavage because it has been reported that T. acidophilum tRNA contains m⁷G, which is generally not found in archaeal tRNAs. RNA sequencing and liquid chromatography–mass spectrometry revealed that the m⁷G modification exists at a novel position 49. Furthermore, we found several distinct modifications, which have not previously been found in archaeal tRNA, such as 4-thiouridine9, archaeosine13 and 5-carbamoylmethyuridine34. The related tRNA modification enzymes and their genes are discussed.     

Microbiological Studies of Coli-aerogenes Bacteria

The presence of glucose-6-phosphate markedly stimulated the anaerobic utilization of glyoxylate by either cell-free extracts or partially purified enzyme preparations of coli-aerogenes bacteria. The enzymic reduction of glyoxylate to glycollate was found to occur in the presence of TPN with the following substrates; glucose-6-phosphate, glucose plus ATP, gluconate plus ATP, glucose-1-phosphate or malate. The data indicated that the reduction of glyoxylate to glycollate was coupled to the oxidation of glucose-6-phosphate via the hexose monophosphate shunt pathway. It was propounded that the operation of the hexose monophosphate oxidative pathway might be controlled by TPN-linked glyoxylic reductase, and the mechanisms of enzymic regulation in microbial respiration were also discussed.     

Sequence boundary and related sedimentary and diagenetic facies formed on Middle Permian mid-oceanic carbonate platform: Core observation of Akiyoshi Limestone,Southwest Japan

Detailed core observation of the Akiyoshi Limestone, Southwest Japan, reveals a sequence boundary and related sedimentary and diagenetic facies formed on a late Murgabian (Middle Permian) mid-oceanic carbonate platform. The sequence boundary lies upon karstified bioclastic grainstone and is overlain by peritidal lime- and dolo-mudstone. The karstified bioclastic grainstone, which had been affected by subaerial exposure and early diagenetic processes, is characterized by crystal silts, prismatic, bladed and dogtooth cements, blackened limestone features, and alveolar textures. The overlying peritidal lime- and dolo-mudstone is 8 m thick and exhibits fenestrae, fissures, laminations, black pebbles, and low-diversity biota composed exclusively of ostracodes and calcispherids. The sequence boundary almost coincides with a major fusulinoidean biostratigraphic boundary. A sea-level fall in the late Murgabian resulted in a biotic turnover and formed the sequence boundary and the karst textures. The following relatively slow transgression resulted in the deposition of the thick transgressive peritidal unit.     

Fourier transform infared spectroscopy investigation of protein conformation in spray-dried protein/trehalose powders

Spray drying is a way to generate protein solids (powders), which is also true for lyophilization. Sugars are used to protect proteins from conformational changes and chemical degradations arising from drying processes and storage conditions such as the humidity. The influence of trehalose and humidity on the conformation and hydration of spray-dried recombinant human granolucyte colony stimulating factor (rhG-CSF) and recombinant consensus interferon-alpha (rConIFN) was investigated using Fourier transform IR spectroscopy. The spectral analysis of spray-dried powders in the amide I region demonstrated that trehalose stabilized the alpha-helical conformation of both rhG-CSF and rConIFN proteins. Exposure of the pure protein powders to 33% relative humidity (RH) resulted in the formation of beta sheets and loss of turns but no change in alpha-helical structure. Trehalose reduced the magnitude of the changes in beta sheets and turns. Exposure of the pure protein powders to 75% RH resulted in the loss of alpha-helical conformation with a corresponding increase in beta structures (beta sheets and turns). Trehalose did not protect proteins from the loss of alpha-helical structures, but it reduced the formation of antiparallel beta sheets. Hydrogen-deuterium exchange (H-D exchange) was used to further characterize these hydration-induced conformational changes. At 33% RH the percent exchange of the protein decreased with increasing trehalose content, indicating a greater protection of the protein from H-D exchange by a higher concentration of trehalose. Such protection correlates with decreased conformational changes of the protein by trehalose at this humidity. At 75% RH the degree of H-D exchange of the protein was insensitive to the powder composition in all powders. Surprisingly, the H-D exchange of trehalose was low at about 20-25%, which was nearly independent of the protein/trehalose ratio and humidity, indicating that the exchangeable protons on trehalose molecules are highly protected in protein-containing powders. The observed protein hydration is related to the effect of trehalose on the conformational changes of the protein under humidity.     

Cohesin-dockerin interactions within and between Clostridium josui and Clostridium thermocellum: binding selectivity between cognate dockerin and cohesin domains and species specificity

The cellulosome components are assembled into the cellulosome complex by the interaction between one of the repeated cohesin domains of a scaffolding protein and the dockerin domain of an enzyme component. We prepared five recombinant cohesin polypeptides of the Clostridium thermocellum scaffolding protein CipA, two dockerin polypeptides of C. thermocellum Xyn11A and Xyn10C, four cohesin polypeptides of Clostridium josui CipA, and two dockerin polypeptides of C. josui Aga27A and Cel8A, and qualitatively and quantitatively examined the cohesin-dockerin interactions within C. thermocellum and C. josui, respectively, and the species specificity of the cohesin-dockerin interactions between these two bacteria. Surface plasmon resonance (SPR) analysis indicated that there was a certain selectivity, with a maximal 34-fold difference in the K(D) values, in the cohesin-dockerin interactions within a combination of C. josui, although this was not detected by qualitative analysis. Affinity blotting analysis suggested that there was at least one exception to the species specificity in the cohesin-dockerin interactions, although species specificity was generally conserved among the cohesin and dockerin polypeptides from C. thermocellum and C. josui, i.e. the dockerin polypeptides of C. thermocellum Xyn11A exceptionally bound to the cohesin polypeptides from C. josui CipA. SPR analysis confirmed this exceptional binding. We discuss the relationship between the species specificity of the cohesin-dockerin binding and the conserved amino acid residues in the dockerin domains.     

Vertical distribution, population structure and life history of Thysanoessa longipes (Crustacea: Euphausiacea) around Yamato Rise, central Japan Sea

The diel vertical migration, growth and spawning season of theeuphausiid, Thysanoessa longipes, were investigated using seasonalsamples collected from waters around the Yamato Rise, centralJapan Sea, during the period 1987 to 1999. Thysanoessa longipeswas present throughout a broad bathymetric layer extending downas deep as 1000 m. There was a clear trend for larger specimensto occur at deeper depths. The peak of abundance of the totalpopulation occurred at depths of 30–300 m at night, and150–500 m during the day, and the distance of the dielvertical migrations of the total population was estimated tobe between 100 and 150 m. Population structure analysis revealedthe occurrence of three cohorts aged 0+, 1+ and 2+ years, withfemales attaining a larger body size than males. Growth as determinedby body length was found to fit well to the von Bertalanffygrowth equation. The estimated life span for males and femalesis 3 years, and females reach maturity in 2 years. Based onthe occurrence of calyptopis larvae, spawning of T. longipeswas estimated to occur over only a limited period of the yearbetween April and May.     

Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride

This study was carried out to investigate the structural perturbation of the protein's local structure by the denaturants under non-denaturing conditions. Crystal structure of CutA from an archaeon Pyrococcus horikosii (PhoCutA), a heavy-metal binding protein, was determined at 1.6-angstroms resolution in the presence of 3 M guanidine HCl (GdnHCl). Native PhoCutA has a large number of short intramolecular hydrogen bonds and salt bridges on the protein surface, of which greater than 90% of hydrogen bonds and all salt bridges were retained in 3 M GdnHCl. Hydrogen bonds that disappeared in the GdnHCl crystal structure were mainly located on the protein surface, especially around the structurally perturbed loop, suggesting interactions between peptide groups and GdnHCl. Only a few GdnH+ ions were observed in the crystal structure, although none at the surface, of the protein. Two GdnH+ ions were observed in the center of the trimeric structure, replacing water molecules, and were hydrogen bonded with Asp84 and Asp86 of each chain. The exterior loop from Tyr39 to Lys44, including Trp40-Trp41, was perturbed structurally. Decreases in temperature factors were observed in beta strand 5 and the N terminus of helix 3. These results suggest the specific bindings of GdnH+ with some acidic residues and the non-specific bindings around Trp residues and peptide groups on the protein surface and that binding of GdnHCl to the native protein is limited, resulting in local structural perturbation.     

Characterization of Paecilomycescinnamomeus from the camellia whitefly, Aleurocanthus camelliae (Hemiptera: Aleyrodidae), infesting tea in Japan

The whitefly, Aleurocanthus camelliae Kanmiya and Kasai (Hemiptera: Aleyrodidae), is an invasive species in Japan that was first discovered in 2004 on tea in Kyoto. Soon after its arrival epizootics of an entomopathogenic fungus were observed in populations of the whitefly in many tea-growing regions. Here we identify this fungus as Paecilomyces cinnamomeus (Petch) Samson and W. Gams (Hypocreales: Clavicipitaceae) based on morphological characteristics and molecular analyses. This is the first record of P. cinnamomeus in Japan and also the first time it has been recorded from the genus Aleurocanthus. A isolate of P. cinnamomeus caused greater than 50% and 90% infection in whitefly nymphs at 1 × 10⁶ and 1 × 10⁷ conidia/ml respectively, while the commercial mycoinsecticides Preferd® (Isaria fumosorosea) and Mycotal® (Lecanicillium muscarium) caused <10% infection at their recommended field rates (5 × 10⁶ and 9 × 10⁶ conidia/ml, respectively), suggesting that P. cinnamomeus may be more useful as a control agent than the currently available mycoinsecticides. Optimum and upper limit temperatures for in vitro growth of P. cinnamomeus isolates were 22.5–25 °C and 32.5 °C, respectively. At field rates, the fungicide thiophanate-methyl caused some inhibition of in vitro growth of P. cinnamomeus isolates, and the bactericide copper oxychloride and the insecticides tolfenpyrad and methidathion were strongly inhibitory. The findings obtained in this study will be useful in the development of microbial control programs using P. cinnamomeus against A. camelliae.     

Endogenous synthesis of prostacyclin was positively regulated during the maturation phase of cultured adipocytes

Prostacyclin alternatively called prostaglandin (PG) I₂ is an unstable metabolite synthesized by the arachidonate cyclooxygenase pathway. Earlier studies have suggested that prostacyclin analogues can act as a potent effector of adipose differentiation. However, biosynthesis of PGI₂ has not been determined comprehensively at different life stages of adipocytes. PGI₂ is rapidly hydrolyzed to the stable product, 6-keto-PGF_1α, in biological fluids. Therefore, the generation of PGI₂ can be quantified as the amount of 6-keto-PGF_1α. In this study, we attempted to develop a solid-phase enzyme-linked immunosorbent assay (ELISA) using a mouse antiserum specific for 6-keto-PGF_1α. According to the typical calibration curve of our ELISA, 6-keto-PGF_1α can be quantified from 0.8 pg to 7.7 ng in an assay. The evaluation of our ELISA revealed the higher specificity of our antiserum without the cross-reaction with other related prostanoids while it exhibited only the cross-reaction of 1.5 % with PGF_2α. The resulting ELISA was applied to the quantification of 6-keto-PGF_1α generated endogenously by cultured 3T3-L1 cells at different stages. The cultured cells showed the highest capability to generate 6-keto-PGF_1α during the maturation phase of 4–6 days, which was consistent with the coordinated changes in the gene expression of PGI synthase and the IP receptor for PGI₂. Following these events, the accumulation of fats was continuously promoted up to 14 days. Thus, our immunological assay specific for 6-keto-PGF_1α is useful for monitoring the endogenous levels of the unstable parent PGI₂ at different life stages of adipogenesis and for further studies on the potential association with the up-regulation of adipogenesis in cultured adipocytes.     

Progress in the 21st century: a Roadmap for the Ecological Society of Japan

The primary goal of the 60th anniversary symposium of the Ecological Society of Japan (ESJ) was to re-examine the role of the Society. The first of five lectures, “Development of Long-term Ecological Research in Japan,” discussed the increasingly important role of long-term and networked research studies. Ecological research in Asia faces many challenges, because Asia features natural and anthropogenic landscapes with highly diverse ecosystems. “Developing Strategies of the Ecological Society of Japan for Worldwide Societies of Ecology with Special Reference to Strategies for Asia” emphasized the role of ESJ in promoting ecological research and outreach in Asia. Ecosystem sustainability is a key issue in both the theory and practice of ecosystem management. A framework concept of an environmental and biodiversity cycle was proposed in the session “Linking Community and Ecosystem Dynamics” for understanding the mechanisms driving the sustainability of ecosystems. Ecosystem services are essential aspects of land use and conservation planning and management. “Integrating Models of Ecosystem Services and Land Use Changes” reviewed recently-developed models that simulate patterns of land-use change and analyze its effects on ecosystem services and also recommended future directions for collaboration among researchers. “Disaster Resilience and Coastal Ecology” highlighted the contributions of ecologists to evaluating the resilience of damaged coastal ecosystems and provided sound proposals to local communities and governments for rehabilitation plans. The past achievements and future directions of ESJ were discussed by the panelists and the audience in “Past and Future of the Ecological Society of Japan.”