Chirping and Sudden Excitation of Energetic-Particle-Driven Geodesic Acoustic Modes in a Large Helical Device Experiment

Energetic-particle-driven geodesic acoustic modes (EGAMs) observed in a Large Helical Device experiment are investigated using a hybrid simulation code for energetic particles interacting with a magnetohydrodynamic (MHD) fluid. The frequency chirping of the primary mode and the sudden excitation of the half-frequency secondary mode are reproduced for the first time with the hybrid simulation using the realistic physical condition and the three-dimensional equilibrium. Both EGAMs have global spatial profiles which are consistent with the experimental measurements. For the secondary mode, the bulk pressure perturbation and the energetic particle pressure perturbation cancel each other out, and thus the frequency is lower than the primary mode. It is found that the excitation of the secondary mode does not depend on the nonlinear MHD coupling. The secondary mode is excited by energetic particles that satisfy the linear and nonlinear resonance conditions, respectively, for the primary and secondary modes

Simulation of energetic particle driven geodesic acoustic modes and the energy channeling in the Large Helical Device plasmas

Energetic particle driven geodesic acoustic modes (EGAMs) in Large Helical Device plasmas are investigated using MEGA code. MEGA is a hybrid simulation code for energetic particles interacting with a magneto-hydrodynamic (MHD) fluid and in the present work, both the energetic particles and bulk ions are described by the kinetic equations. The low frequency EGAMs are reproduced. Also, the energy transfer is analyzed and the bulk ion heating during the EGAM activity is observed. The ions obtain energy when the energetic particleslose energy, and this indicates that an energy channel is established by the EGAM. EGAM channeling is reproduced by simulation with realistic parameters for the first time. The heating power to bulk ions is 3.4 kW m−3. It is found that sideband resonance is dominant during the energy transfer from EGAM to the bulk ions, and the transit frequencies of resonant bulk ions are one-half of the EGAM frequency

The systematic investigation of energetic-particle-driven geodesic acoustic mode channeling using MEGA code

Energetic-particle-driven geodesic acoustic modes (EGAMs) channeling in the Large Helical Device (LHD) plasmas are systematically investigated for the first time using MEGA code. MEGA is a hybrid simulation code for energetic particles interacting with a magnetohydrodynamic (MHD) fluid. In the present work, both the energetic particles and the bulk ions are described kinetically. The EGAM profiles in the three-dimensional form is illustrated. Then, EGAM channeling behaviors are analyzed under different conditions. During the EGAM activities without frequency chirping, EGAM channeling occurs in the linear growthstage but terminates in the decay stage after the saturation. During the EGAM activities with frequency chirping, EGAM channeling occurs continuously. Also, low-frequency EGAM makes the energy transfer efficiency (Eion/EEP) higher, and this is confirmed by changing the energetic particle pressure, energetic particle beam velocity, and energetic particle pitch angle. Moreover, higher bulk ion temperature makes the energy transfer efficiency higher. In addition, under acertain condition, the energy transfer efficiency in the deuterium plasma is lower than that in the hydrogen plasma

High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library

<p>Abstract</p> <p>Background</p> <p>During the last two decades, DNA sequencing has led to the identification of numerous genes in key species; however, in most cases, their functions are still unknown. In this situation, reverse genetics is the most suitable method to assign function to a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse-genetic strategy that combines random chemical mutagenesis with high-throughput discovery of the induced mutations in target genes. The method has been applied to a variety of plant and animal species. Screening of the induced mutations is the most important step in TILLING. Currently, direct sequencing or nuclease-mediated screening of heteroduplexes is widely used for detection of mutations in TILLING. Both methods are useful, but the costs are substantial and turnaround times are relatively long. Thus, there is a need for an alternative method that is of higher throughput and more cost effective.</p> <p>Results</p> <p>In this study, we developed a high resolution melting (HRM) assay and evaluated its effectiveness for screening ENU-induced mutations in a medaka TILLING library. We had previously screened mutations in the <it>p53 </it>gene by direct sequencing. Therefore, we first tested the efficiency of the HRM assay by screening mutations in <it>p53</it>, which indicated that the HRM assay is as useful as direct sequencing. Next, we screened mutations in the <it>atr </it>and <it>atm </it>genes with the HRM assay. Nonsense mutations were identified in each gene, and the phenotypes of these nonsense mutants confirmed their loss-of-function nature.</p> <p>Conclusions</p> <p>These results demonstrate that the HRM assay is useful for screening mutations in TILLING. Furthermore, the phenotype of the obtained mutants indicates that medaka is an excellent animal model for investigating genome stability and gene function, especially when combined with TILLING.</p

Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6–4) photoproduct and their use in (6–4) photolyase studies

The pyrimidine(6–4)pyrimidone photoproduct, a major UV lesion formed between adjacent pyrimidine bases, is transformed to its Dewar valence isomer upon exposure to UVA/UVB light. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3′–5′)thymidine site and incorporated it into oligodeoxyribonucleotides. The diastereoisomers of the partially protected dinucleoside monophosphate bearing the (6–4) photoproduct, which were caused by the chirality of the phosphorus atom, were separated by reversed-phase chromatography, and the (6–4) photoproduct was converted to the Dewar photoproduct by irradiation of each isomer with Pyrex-filtered light from a high-pressure mercury lamp. The Dewar photoproduct was stable under both acidic and alkaline conditions at room temperature. After characterization of the isomerized base moiety by NMR spectroscopy, a phosphoramidite building block was synthesized in three steps. Although the ordinary method could be used for the oligonucleotide synthesis, benzimidazolium triflate as an alternative activator yielded better results. The oligonucleotides were used for the analysis of the reaction and the binding of Xenopus (6–4) photolyase. Although the affinity of this enzyme for the Dewar photoproduct-containing duplex was reportedly similar to that for the (6–4) photoproduct-containing substrate, the results suggested a difference in the binding mode

Development of ethnographic digital collections

Περιέχει το πλήρες κείμενοΟι λαογραφικές συλλογές αποτελούν πολύτιμη πηγή μελέτης, εξερεύνησης και αξιολόγησης των εθνικών στερεοτύπων των διαφόρων διαμερισμάτων μιας χώρας, δεδομένου ότι στις συλλογές είναι καταχωρημένα ανόθευτα και πηγαία τα εγχώρια εθνοχαρακτηριστικά τους. Κατά κύριο λόγο η λαογραφία αναφέρεται στους μύθους, τα τραγούδια, τη μουσική, τα έθιμα, τη χειροτεχνία, την ενδυμασία, την αρχιτεκτονική και την προφορική παράδοση μιας κοινότητας. Η ιδιαιτερότητα και η ποικιλία ενός τομέα όπως της λαογραφίας δικαιολογεί απόλυτα την ύπαρξη συλλογών και υπο-συλλογών σύνθετης δομής και σημασιολογίας, όπως αυτές που αναφέρουμε παραπάνω. Επομένως η ανάπτυξη ψηφιακών συλλογών απαιτεί τη διατήρηση των στοιχείων που χρειάζονται για: (α) την περιγραφή του περιεχομένου της κάθε συλλογής χωριστά και (β) τη σωστή απεικόνιση της δομής των αντικειμένων στο εσωτερικό αυτής. Στόχος της εργασίας αυτής είναι η παρουσίαση μιας μεθοδολογίας για την ανάπτυξη ενός περιγραφικού μοντέλου μεταδεδομένων για λαογραφικές συλλογές. Το μοντέλο θα αποτελέσει βασικό εργαλείο για την περιγραφή του ψηφιοποιημένου λαογραφικού υλικού, την πρόσβαση σε αυτό από κατανεμημένους χρήστες και φυσικά την επικοινωνία του με άλλα συστήματα. Επιπλέον θα συμβάλλει στη διασύνδεση σύνθετων συλλογών και των αντικειμένων που περιλαμβάνουν είτε σημασιολογικά, είτε χρονικά, είτε θεματικά είτε με οποιονδήποτε άλλο τρόπο απαιτεί η φύση των συλλογών και οι ανάγκες των χρηστών

ATF6α/β-mediated adjustment of ER chaperone levels is essential for development of the notochord in medaka fish.

ATF6α and ATF6β are membrane-bound transcription factors activated by regulated intramembrane proteolysis in response to endoplasmic reticulum (ER) stress to induce various ER quality control proteins. ATF6α- and ATF6β single-knockout mice develop normally, but ATF6α/β double knockout causes embryonic lethality, the reason for which is unknown. Here we show in medaka fish that ATF6α is primarily responsible for transcriptional induction of the major ER chaperone BiP and that ATF6α/β double knockout, but not ATF6α- or ATF6β single knockout, causes embryonic lethality, as in mice. Analyses of ER stress reporters reveal that ER stress occurs physiologically during medaka early embryonic development, particularly in the brain, otic vesicle, and notochord, resulting in ATF6α- and ATF6β-mediated induction of BiP, and that knockdown of the α1 chain of type VIII collagen reduces such ER stress. The absence of transcriptional induction of several ER chaperones in ATF6α/β double knockout causes more profound ER stress and impaired notochord development, which is partially rescued by overexpression of BiP. Thus ATF6α/β-mediated adjustment of chaperone levels to increased demands in the ER is essential for development of the notochord, which synthesizes and secretes large amounts of extracellular matrix proteins to serve as the body axis before formation of the vertebra

Generation of medaka gene knockout models by target-selected mutagenesis

We have established a reverse genetics approach for the routine generation of medaka (Oryzias latipes) gene knockouts. A cryopreserved library of N-ethyl-N-nitrosourea (ENU) mutagenized fish was screened by high-throughput resequencing for induced point mutations. Nonsense and splice site mutations were retrieved for the Blm, Sirt1, Parkin and p53 genes and functional characterization of p53 mutants indicated a complete knockout of p53 function. The current cryopreserved resource is expected to contain knockouts for most medaka genes