Metabolic balance of streams draining urban and agricultural watersheds in central Japan

Empirical data that describe the metabolic balance of stream ecosystems in human-dominated watersheds are scarce. We measured ecosystem metabolism in 23 open-canopied lowland streams draining urban and agricultural areas in the Fuji River Basin, central Japan. Gross primary production (GPP) and community respiration (CR) were estimated using the diurnal dissolved oxygen (DO) change technique, with the reaeration coefficient (K ₂) determined from seven empirical depth-velocity equations. Because the predicted values of K ₂ showed variation among the depth-velocity equations, the estimates of stream metabolism also varied according to the equations. However, CR was almost always greater than GPP, resulting in negative net ecosystem production (NEP) and GPP/CR ratios below unity for most of the study reaches. Highly heterotrophic streams were found in intensively farmed watersheds, suggesting that organic matter loading from agricultural lands is likely to be a source of allochthonous carbon fueling excess respiration in the study streams. In contrast, streams draining more urbanized areas were less heterotrophic. The present results suggest that lowland streams in agriculturally developed watersheds are associated strongly with terrestrial ecosystems as a source of organic carbon. The resultant strong respiration might become the dominant process in ecosystem metabolism, as reported for headwater streams, large downstream rivers, and estuaries.     

Evaluation of functional groups on amino acids in cyclic tetrapeptides in histone deacetylase inhibition

The naturally occurring cyclic tetrapeptide, chlamydocin, originally isolated from fungus Diheterospora chlamydosphoria, consists of α-aminoisobutyric acid, l-phenylalanine, d-proline and an unusual amino acid (S)-2-amino-8-((S)-oxiran-2-yl)-8-oxooctanoic acid (Aoe) and inhibits the histone deacetylases (HDACs), a class of regulatory enzymes. The epoxyketone moiety of Aoe is the key functional group for inhibition. The cyclic tetrapeptide scaffold is supposed to play important role for effective binding to the surface of enzymes. In place of the epoxyketone group, hydroxamic acid and sulfhydryl group have been applied to design inhibitor ligands to zinc atom in catalytic site of HDACs. In the research for more potent HDAC inhibitors, we replaced the epoxyketone moiety of Aoe with different functional groups and synthesized a series of chlamydocin analogs as HDAC inhibitors. Among the functional groups, methoxymethylketone moiety showed as potent inhibition as the hydroxamic acid. On the contrary, we confirmed that borate, trifruoromethylketone, and 2-aminoanilide are almost inactive in HDAC inhibition.     

Cyclic tetrapeptides with –SS– bridging between amino acid side chains for potent histone deacetylases’ inhibition

Cyclic depsipeptide FK228 with an intramolecular disulfide bond is a potent inhibitor of histone deacetylases (HDAC). FK228 is stable in blood because of its prodrug function, whose –SS– bond is reduced within the cell. Here, cyclic peptides with –SS– bridges between a variety of amino acids were synthesized and assayed for HDAC inhibition. Cyclic peptide 3, cyclo(-l-amino acid-l-amino acid-l-Val-d-Pro-), with an –SS– bridge between the first and second amino acids, was found to be a potent HDAC inhibitor. Cyclic peptide 7, cyclo(-l-amino acid-d-amino acid-l-Val-d-Pro-), with an –SS– bridge between the first and second amino acids, was also a potent HDAC inhibitor.     

Responses of leaf gas exchange, water relations, and water consumption in seedlings of four semiarid tree species to soil drying

To understand the response patterns to soil drying and the water use properties of commonly reforested trees in the semiarid Loess Plateau region of China, a glasshouse experiment was carried out with the seedlings of four species, i.e., Robinia pseudoacacia, Armeniaca sibirica, Syringa oblata, and Quercus liaotungensis. Severe water stress induced by withholding water resulted in permanent wilting of most of the seedlings pot-cultured with sandy soil in 8–12 days. Predawn and midday leaf water potentials and gas exchange characteristics (e.g., stomatal conductance) in the seedlings did not show marked changes until the volumetric soil water content decreased to about 0.05. As the soil water content decreased further, these physiological parameters rapidly declined, approaching their minimal levels at the stage of permanent wilting. The response of each parameter to soil water content changes was fitted with a non-linear saturation curve. Though the results suggested that the general pattern of responses to soil drying was identical among the species, quantitative differences in drought tolerance and water use properties were detected. Leaf stomatal conductance in R. pseudoacacia and A. sibirica showed earlier responses to reduced predawn leaf water potentials. However, water use characteristics and specific leaf area indicated that these two species consumed more water and may not be as drought tolerant as S. oblata and Q. liaotungensis. These results may provide important information to compare the reforestation species with respect to soil drying.     

Cyclic tetrapeptides with thioacetate tails or intramolecular disulfide bridge as potent inhibitors of histone deacetylases

Two thioacetate tails were introduced to the chlamydocin- and CHAP31-related cyclic tetrapeptides. An intramolecular disulfide bridge could be formed in the CHAP31-related cyclic peptides. Both the thioacetate-tailed and disulfide-bridged peptides were potent histone deacetylase inhibitors in the presence of sulfhydryl compound. Potent p21 promoter inducing activity was also observed in vivo.     

Purification of human and avian influenza viruses using cellulose sulfate ester (Cellufine Sulfate) in the process of vaccine production

Affinity chromatography using sulfated, spherical cellulose beads (Cellufine Sulfate) was assessed for purification of influenza A and influenza B viruses. Recovery rates of viruses eluted from the beads were high for all tested virus strains. This method was also useful for removing chicken egg-derived impurities from allantoic fluids containing influenza viruses; the hemagglutination activity per amount of protein in the eluted sample was significantly higher than that in the applied sample. These results suggest that use of Cellufine Sulfate is a practical method for primary purification of influenza viruses in the process of influenza vaccine production.     

Synthesis,evaluation and molecular modeling of cyclic tetrapeptide histone deacetylase inhibitors as anticancer agents

Histone deacetylase inhibitors (HDACIs) are a promising class of anticancer agents. To examine whether a slight change in the recognition domain could alter their inhibitory activity, we synthesized a series of cyclo(?l ‐Am7(S2Py)‐Aib‐l ‐Phe(n‐Me)‐d ‐Pro)derivatives and evaluated their HDAC inhibitory and anticancer activities. The peptides exhibited potent HDAC inhibitory activity and inhibited three human cancer cell lines with IC₅₀ in the micromolar range. Docking and molecular dynamics simulation were conducted to explore the interaction mechanisms of class I and II HDACs with these inhibitors. It revealed that the zinc ion in the active site coordinated five atoms of HDACs and the sulfur atom of the inhibitor. The metal binding domains of these compounds interacted with HDAC2, and the surface recognition domains of these compounds interacted with HDAC4 through hydrogen bonding. The hydrophobic interactions also provided favorable contributions to stabilize the complexes. The results obtained from this study would be helpful for us to design some novel cyclic tetrapeptides that may act as potent HDACIs. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Kinetic analysis of the entire RNA amplification process by Qbeta replicase

The kinetics of the RNA replication reaction by Qbeta replicase were investigated. Qbeta replicase is an RNA-dependent RNA polymerase responsible for replicating the RNA genome of coliphage Qbeta and plays a key role in the life cycle of the Qbeta phage. Although the RNA replication reaction using this enzyme has long been studied, a kinetic model that can describe the entire RNA amplification process has yet to be determined. In this study, we propose a kinetic model that is able to account for the entire RNA amplification process. The key to our proposed kinetic model is the consideration of nonproductive binding (i.e. binding of an enzyme to the RNA where the enzyme cannot initiate the reaction). By considering nonproductive binding and the notable enzyme inactivation we observed, the previous observations that remained unresolved could also be explained. Moreover, based on the kinetic model and the experimental results, we determined rate and equilibrium constants using template RNAs of various lengths. The proposed model and the obtained constants provide important information both for understanding the basis of Qbeta phage amplification and the applications using Qbeta replicase.