Carbon cycling and budget in a forested basin of southwestern Hokkaido,northern Japan

Quantification of annual carbon sequestration is very important in order to assess the function of forest ecosystems in combatting global climate change and the ecosystem responses to those changes. Annual cycling and budget of carbon in a forested basin was investigated to quantify the carbon sequestration of a cool-temperate deciduous forest ecosystem in the Horonai stream basin, Tomakomai Experimental Forest, northern Japan. Net ecosystem exchange, soil respiration, biomass increment, litterfall, soil-solution chemistry, and stream export were observed in the basin from 1999–2001 as a part of IGBP-TEMA project. We found that 258 g C m^–2 year^–1 was sequestered annually as net ecosystem exchange (NEE) in the forested basin. Discharge of carbon to the stream was 4 g C m^–2 year^–1 (about 2% of NEE) and consisted mainly of dissolved inorganic carbon (DIC). About 43% of net ecosystem productivity (NEP) was retained in the vegetation, while about 57% of NEP was sequestered in soil, suggesting that the movement of sequestered carbon from aboveground to belowground vegetation was an important process for net carbon accumulation in soil. The derived organic carbon from aboveground vegetation that moved to the soil mainly accumulated in the solid phase of the soil, with the result that the export of dissolved organic carbon to the stream was smaller than that of dissolved inorganic carbon. Our results indicated that the aboveground and belowground interaction of carbon fluxes was an important process for determining the rate and retention time of the carbon sequestration in a cool-temperate deciduous forest ecosystem in the southwestern part of Hokkaido, northern Japan.     

PRIME: automatically extracted PRotein Interactions and Molecular Information databasE

With the exponentially increasing amount of information in the biomedical field, the significance of advanced information retrieval and information extraction, as well as the role of databases, has been increasing. PRIME is an integrated gene/protein informatics database based on natural language processing. It provides automatically extracted protein/family/gene/compound interaction information including both physical and genetic interactions, gene ontology based functions, and graphic pathway viewers. Gene/protein/family names and functional terms are recognized based on dictionaries developed in our laboratory. The interaction and functional information are extracted by syntactic dependencies and various phrase patterns. We have included about 920,000 (non-redundant) protein interactions and 360,000 annotated gene-function relationships for major eukaryotes. By combining the sequence and text information, the pathway comparison between two organisms and simple pathway deduction based on other organism interaction data, and pathway filtering using tissue expression data, are also available. This database is accessible at http://prime.ontology.ims.u-tokyo.ac.jp:8081.     

A guideline for ecological risk management procedures

A practical guideline for community-level ecological risk management is proposed, with particular emphasis on the mutual interdependencies of the scientific analysis, public consensus building, and an adaptive management. The procedure we recommend spans the screening of potential ecological risks, the involvement of related stakeholders, the conceptual development from the undesired event over assessment endpoints to measures of effect and stress factors, the risk assessment for the no-action case, the planning phase from the public decision to become active and the setting of goals over a specification of monitoring and control methods to an assessment of feasibility and a public approval of the management plan and finally the adaptive management from initiation over continued monitoring to revisions of the plan, if required. The procedure contains several checkpoints, alternative routes, and possibilities to correct previous decisions.     

ATPase activity of p97/valosin-containing protein is regulated by oxidative modification of the evolutionally conserved cysteine 522 residue in Walker A motif

Valosin-containing protein (p97/VCP) has been proposed as playing crucial roles in a variety of physiological and pathological processes such as cancer and neurodegeneration. We previously showed that VCP(K524A), an ATPase activity-negative VCP mutant, induced vacuolization, accumulation of ubiquitinated proteins, and cell death, phenotypes commonly observed in neurodegenerative disorders. However, any regulatory mechanism of its ATPase activity has not yet been clarified. Here, we show that oxidative stress readily inactivates VCP ATPase activity. With liquid chromatography/tandem mass spectrometry, we found that at least three cysteine residues were modified by oxidative stress. Of them, the 522nd cysteine (Cys-522) was identified as the site responsible for the oxidative inactivation of VCP. VCP(C522T), a single-amino acid substitution mutant from cysteine to threonine, conferred almost complete resistance to the oxidative inactivation. In response to oxidative stress, VCP strengthened the interaction with Npl4 and Ufd1, both of which are essential in endoplasmic reticulum-associated protein degradation. Cys-522 is located in the second ATP binding motif and is highly conserved in multicellular but not unicellular organisms. Cdc48p (yeast VCP) has threonine in the corresponding amino acid, and it showed resistance to the oxidative inactivation in vitro. Furthermore, a yeast mutant (delta cdc48 + cdc48[T532C]) was shown to be susceptible to oxidants-induced growth inhibition and cell death. These results clearly demonstrate that VCP ATPase activity is regulated by the oxidative modification of the Cys-522 residue. This regulatory mechanism may play a key role in the conversion of oxidative stress to endoplasmic reticulum stress response in multicellular organisms and also in the pathological process of various neurodegenerative disorders.     

Production of 1,2-didocosahexaenoyl phosphatidylcholine by bonito muscle lysophosphatidylcholine/transacylase

1,2-Didocosahexaenoyl phosphatidylcholine (PC), which has highly unsaturated fatty acid at both sn-1 and sn-2 positions of glycerol, is a characteristic molecular species of bonito muscle. To examine the involvement of a de novo route in its synthesis, the molecular species of phosphatidic acid (PA) were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-olato dizinc(II) complex, a novel phosphate-capture molecule. However, 1,2-didocosahexaenoyl species could not be detected. Next, 1,2-didocosahexaenoyl PC synthesis by the cytosolic lysophosphatidylcholine (LPC)/transacylase was examined using endogenous LPC from bonito muscle, in which the 2-docosahexaenoyl species is abundant. The LPC/transacylase synthesized 1,2-didocosahexaenoyl PC as the most abundant molecular species. For further characterization, the LPC/transacylase was purified to homogeneity from the 100,000 x g supernatant of bonito muscle. The isolated LPC/transacylase is a labile glycoprotein with molecular mass of 52 kDa including a 5-kDa sugar moiety. The LPC/transacylase showed a PC synthesis (transacylase activity) below and above the critical micelle concentration of substrate LPC, and fatty acid release (lysophospholipase activity) was always smaller than the transacylase activity, even with a monomeric substrate. These results suggest that the LPC/transacylase is responsible for the synthesis of 1,2-didocosahexaenoyl PC.     

Coexposure to benzo[a]pyrene plus UVA induced DNA double strand breaks: visualization of Ku assembly in the nucleus having DNA lesions

Benzo[a]pyrene (BaP) is a ubiquitous environmental pollutant with potential carcinogenicity. It has been shown that BaP, upon UVA irradiation, synergistically induced oxidative DNA damage, but other DNA damage was not confirmed. In this study, we examined whether coexposure to BaP plus UVA induces double strand breaks (DSBs) using xrs-5 cells, deficient in the repair of DSBs (Ku80 mutant), and whether Ku translocates involving the formation of DSBs. BaP plus UVA had a significant cytotoxic effect on CHO-K1 cells and an even more drastic effect on Ku80-deficient, xrs-5 cells, suggesting that the DSBs were generated by coexposure to BaP plus UVA. The DSBs were repaired in CHO-K1 cells within 30 min, but not in xrs-5 cells, indicating the involvement of a non-homologous end joining, which needs Ku proteins. Furthermore, we succeeded in visualizing that Ku80 rapidly assembled to the exposed region, in which DSBs might be generated, and clarified that the presence of both Ku70 and Ku80 was important for their accumulation.     

COMPARATIVE STUDY ON THE PHOTOSYNTHETIC PROPERTIES OF PRASIOLA (CHLOROPHYCEAE) AND NOSTOC (CYANOPHYCEAE) FROM ANTARCTIC AND NON‐ANTARCTIC SITES1

The terrestrial cyanobacterium Nostoc commune Vaucher ex Bornet et Flahault occurs worldwide, including in Japan and on the Antarctic continent. The terrestrial green alga Prasiola crispa (Lightf.) Kütz. is also distributed in Antarctica. These two species need to acclimate to the severe Antarctic climate including low ambient temperature and desiccation under strong light conditions. To clarify this acclimation process, the physiological characteristics of the photosynthetic systems of these two Antarctic terrestrial organisms were assessed. The relative rate of photosynthetic electron flow in N. commune collected in Japan and in Antarctica reached maxima at 900 and 1,100 μmol photons · m^?2 · s^?1, respectively. The difference seemed to reflect the presence of high amounts of UV‐absorbing substances within the Antarctic cyanobacterium. On the other hand, the optimal temperatures for photosynthesis at the two locations were 30°C–35°C and 20°C–25°C, respectively. This finding suggested a decreased photosynthetic thermotolerance in the Antarctic strain. P. crispa exhibited desiccation tolerance and dehydration‐induced quenching of PSII fluorescence. Re‐reduction of the photooxidized PSI reaction center, P700, was also inhibited at fully dry states. Photosynthetic electron flow in P. crispa reached a maximum at 20°C–25°C and at a light intensity of 700 μmol photons ? m^?2 ? s^?1. Interestingly, the osmolarity of P. crispa cells suggested that photosynthesis is performed using water absorbed in a liquid form rather than water absorbed from the air. Overall, these data suggest that these two species have acclimated to optimally photosynthesize under conditions of the highest light intensity and the highest temperature for their habitat in Antarctica.     

Hindgut microbes, fermentation and their seasonal variations in Hokkaido native horses compared to light horses

Fecal bacteria and protozoa of Hokkaido native horses and light horses were enumerated to compare seasonal variation in hindgut microbes and fermentation between the two breeds. Fecal samples were collected in winter and summer from eight horses (four for each breed) that had been reared together under the same conditions after birth (on woodland pasture in winter and on grassland pasture for the rest of the year). Total fecal bacteria counts for both breeds showed temporal variation, with the highest levels occurring in summer (P<0.05). For both breeds, Gram-negative rods were the major constituents (58–69%) and showed higher counts in winter (P<0.05) than in summer. Total protozoa counts in both breeds were lower in winter than in summer (P<0.05). The proportion of large cellulolytic protozoa such as Cochliatoxum periachtum was increased (P<0.05) in winter, and this tended to be more pronounced in native horses. Although total volatile fatty acids (VFA) in feces were lower in winter (P<0.05), the reduction was smaller in native horses (P<0.05). Fecal VFA pattern showed a shift toward more acetate and less propionate production in winter regardless of the horse breed. Evaluation of digestive tract organs in 12 animals showed that the relative weight of the colon in body weight or total digestive tract weight is larger in native horses than in light horses (P<0.05). The present results suggest that hindgut microbial adaptation to winter diets occurs to a greater extent in native horses, as partly characterized by advantages in anatomy.