Maintaining Web Applications by Translating Among Different RIA Technologies

As RIA (Rich Internet Application) technologieshave been widely used, the compatibility problem has arisen:they are hardly compatible with each other. To solve theproblem, we have proposed and implemented an automatic RIAtransformation system named Web-IR, which uses anXML-based intermediate representation with a Java-basedframework. As concrete examples, Web-IR currently supportsAjax, Flex, JavaFX, and OpenLaszlo as its input/output. Ourevaluations show that Web-IR can transform existing realapplications into other RIA technologies keeping almost thesame appearances. Finally, we conclude that Web-IR can solvethe problem sufficiently

Effects of clearcutting and girdling on soil respiration and fluxes of dissolved organic carbon and nitrogen in a Japanese cedar plantation

Impacts of forest management practices on soil carbon (C) and nitrogen (N) dynamics remain under debate due to complex interactions between belowground biogeochemical processes. To optimize practices that minimize soil C and N losses, we investigated the effects of management practices on soil C and N fluxes, including the leaching of dissolved organic C (DOC) and N, by comparing clearcutting, stem girdling (removal of the bark and phloem tissue), and control treatments in a Japanese cedar plantation. Canopy opening by clearcutting is hypothesized to have a greater effect on soil C loss and the leaching of nitrate-N relative to girdling. Results showed that clearcutting increased soil heterotrophic respiration (organic matter decomposition) and lead to a loss of soil organic C (2.9–3.7 Mg C ha⁻¹ yr⁻¹). Higher litter inputs from girdled tree dieback caused an increase in DOC fluxes from the organic horizon, whereas the loss of fresh litter inputs decreased DOC fluxes from the organic horizon following clearcutting. Clearcutting increased nitrate-N leaching by 3.3–4.8 kg N ha⁻¹ yr⁻¹ due to the loss of plant N uptake and the increased mineralization of soil organic matter, but high C/N ratios in dissolved organic matter limited nitrate leaching in the girdled treatment. Effects of forest management practices on soil C loss and nitrate leaching loss could be variable, but the slash application in clearcutting and the slow dieback in stem girdling could mitigate soil C loss and nitrate leaching loss

Uncertainties in the nu p-process: supernova dynamics versus nuclear physics

We examine how the uncertainties involved in supernova dynamics as well as in nuclear data inputs affect the nup-process in the neutrino-driven winds. For the supernova dynamics, we find that the wind termination by the preceding dense ejecta shell, as well as the electron fraction (Y_{e, 3}; at 3 10^9 K) play a crucial role. A wind termination within the temperature range of (1.5-3) 10^9 K greatly enhances the efficiency of the nu p-process. This implies that the early wind phase, when the innermost layer of the preceding supernova ejecta is still 200-1000 km from the center, is most relevant to the nup-process. The outflows with Y_{e, 3} = 0.52-0.60 result in the production of the p-nuclei up to A=108 with interesting amounts. Furthermore, the p-nuclei up to A=152 can be produced if Y_{e, 3} = 0.65 is achieved. For the nuclear data inputs, we test the sensitivity to the rates relevant to the breakout from the pp-chain region (A < 12), to the (n, p) rates on heavy nuclei, and to the nuclear masses along the nup-process pathway. We find that a small variation of the rates of triple-alpha and of the (n, p) reaction on 56Ni leads to a substantial change in the p-nuclei production. We also find that 96Pd (N=50) on the nup-process path plays a role as a second seed nucleus for the production of heavier p-nuclei. The uncertainty in the nuclear mass of 82Zr can lead to a factor of two reduction in the abundance of the p-isotope 84Sr.Comment: 20 pages, 22 figures, accepted for publication in Ap

Tryptophan 2,3-dioxygenase is a key modulator of physiological neurogenesis and anxiety-related behavior in mice

Although nutrients, including amino acids and their metabolites such as serotonin (5-HT), are strong modulators of anxiety-related behavior, the metabolic pathway(s) responsible for this physiological modulation is not fully understood. Regarding tryptophan (Trp), the initial rate-limiting enzymes for the kynurenine pathway of tryptophan metabolism are tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO). Here, we generated mice deficient for tdo (Tdo-/-). Compared with wild-type littermates, Tdo-/- mice showed increased plasma levels of Trp and its metabolites 5-hydroxyindoleacetic acid (5-HIAA) and kynurenine, as well as increased levels of Trp, 5-HT and 5-HIAA in the hippocampus and midbrain. These mice also showed anxiolytic modulation in the elevated plus maze and open field tests, and increased adult neurogenesis, as evidenced by double staining of BrdU and neural progenitor/neuronal markers. These findings demonstrate a direct molecular link between Trp metabolism and neurogenesis and anxiety-related behavior under physiological conditions

A Catalytic Role of XoxF1 as La3+-Dependent Methanol Dehydrogenase in Methylobacterium extorquens Strain AM1

In the methylotrophic bacterium Methylobacterium extorquens strain AM1, MxaF, a Ca2+-dependent methanol dehydrogenase (MDH), is the main enzyme catalyzing methanol oxidation during growth on methanol. The genome of strain AM1 contains another MDH gene homologue, xoxF1, whose function in methanol metabolism has remained unclear. In this work, we show that XoxF1 also functions as an MDH and is La3+-dependent. Despite the absence of Ca2+ in the medium strain AM1 was able to grow on methanol in the presence of La3+. Addition of La3+ increased MDH activity but the addition had no effect on mxaF or xoxF1 expression level. We purified MDH from strain AM1 grown on methanol in the presence of La3+, and its N-terminal amino acid sequence corresponded to that of XoxF1. The enzyme contained La3+ as a cofactor. The ΔmxaF mutant strain could not grow on methanol in the presence of Ca2+, but was able to grow after supplementation with La3+. Taken together, these results show that XoxF1 participates in methanol metabolism as a La3+-dependent MDH in strain AM1

High-Energy Electron Transfer Dissociation (HE-ETD) Using Alkali Metal Targets for Sequence Analysis of Post-Translational Peptides

Post-translational modifications (PTMs) of proteins are important in the activation, localization, and regulation of protein function in vivo. The usefulness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) in tandem mass spectrometry (MS/MS) using low-energy (LE) trap type mass spectrometer is associated with no loss of a labile PTM group regarding peptide and protein sequencing. The experimental results of high-energy (HE) collision induced dissociation (CID) using the Xe and Cs targets and LE-ETD were compared for doubly-phosphorylated peptides TGFLT(p)EY(p)VATR (1). Although HE-CID using the Xe target did not provide information on the amino acid sequence, HE-CID using the Cs target provided all the z-type ions without loss of the phosphate groups as a result of HE-ETD process, while LE-ETD using fluoranthene anion gave only z-type ions from z5 to z11. The difference in the results of HE-CID between the Xe and Cs targets demonstrated that HE-ETD process with the Cs target took place much more dominantly than collisional activation. The difference between HE-ETD using Cs targets and LE-ETD using the anion demonstrated that mass discrimination was much weaker in the high-energy process. HE-ETD was also applied to three other phosphopeptides YGGMHRQEX(p)VDC (2: X = S, 3: X = T, 4: X = Y). The HE-CID spectra of the doubly-protonated phosphopeptides (= [M + 2H]2+) of 2, 3, and 4 using the Cs target showed a very similar feature that the c-type ions from c7 to c11 and the z-type ions from z7 to z11 were formed via N–Cα bond cleavage without a loss of the phosphate group

A study on ensuring the quality and safety of pharmaceuticals and medical devices derived from processing of autologous human induced pluripotent stem(-like) cells

As a series of endeavors to establish suitable measures for the sound development of regenerative medicine using human stem cell-based products, we studied scientific principles, concepts, and basic technical elements to ensure the quality and safety of therapeutic products derived from autologous human iPS cells or iPS cell-like cells, taking into consideration scientific and technological advances, ethics, regulatory rationale, and international trends in human stem cell-derived products. This led to the development of the Japanese official Notification No. 0907-4, “Guideline on Ensuring the Quality and Safety of Pharmaceuticals and Medical Devices Derived from the Processing of Autologous Human Induced Pluripotent Stem(-Like) Cells, ” issued by Pharmaceuticals and Food Safety Bureau, Ministry of Health, Labour and Welfare of Japan, on September 7, 2012. The present paper addresses various aspects of products derived from autologous human iPS cells (or iPS cell-like cells), in addition to similar points to consider that are described previously for autologous human stem cell-based products. Major additional points include (1) possible existence of autologous human iPS cell-like cells that are different from iPS cells in terms of specific biological features; (2) the use of autologous human iPS(-like) cells as appropriate starting materials for regenerative medicine, where necessary and significant; (3) establishment of autologous human iPS(-like) cell lines and their characterization; (4) cell banking and/or possible establishment of intermediate cell lines derived from autologous human iPS(-like) cells at appropriate stage(s) of a manufacturing process, if necessary; and (5) concerns about the presence of undifferentiated cells in the final product; such cells may cause ectopic tissue formation and/or tumorigenesis. The ultimate goal of this guidance is to provide suitable medical opportunities as soon as possible to the patients with severe diseases that are difficult to treat with conventional modalities

Identification of Cysteine Proteases and Screening of Cysteine Protease Inhibitors in Biological Samples by a Two-Dimensional Gel System of Zymography and Reverse Zymography

We have developed a two-dimensional (2D-) gel system of zymography and reverse zymography for the detection and characterization of proteases and protease inhibitors. Isoelectric focusing (IEF) agarose gels with pH gradients were employed for separation in the first-dimension and sodium dodecyl sulfate (SDS)-polyacrylamide gel copolymerized with gelatin used for the second dimension. Proteases and protease inhibitors separated by IEF gel were applied on the second gel without trichloroacetic acid (TCA) fixation. Protease activity in the 2D-gel was visualized as transparent spots where gelatin substrate was digested after commassie brilliant blue (CBB) staining. Some of the transparent spots from the skin mucus extract of rainbow trout were determined to be a cysteine protease through use of E-64 or CA-074. In the reverse zymography technique, the gel was incubated with papain solution at 37 ºC for 18 h. Cysteine protease inhibitors from broad bean seeds were detected as clear blue spots after CBB staining. The amino (N-) terminal sequences of four papain inhibitor spots thus detected were demonstrated to be identical to that of favin β chain, a broad bean lectin. Taken together, our system can be considered to be an efficient technique for discovering and characterizing new proteases and protease inhibitors in biological samples. This is the first report describing a 2D-gel system of zymography and reverse zymography