Preceding propagation of turbulence pulses at avalanche events in a magnetically confined plasma.

The preceding propagation of turbulence pulses has been observed for the first time in heat avalanche events during the collapse of the electron internal transport barrier (e-ITB) in the Large Helical Device. The turbulence and heat pulses are generated near the foot of the e-ITB and propagate to the peripheral region within a much shorter time than the diffusion timescale. The propagation speed of the turbulence pulse is approximately 10 km/s, which is faster than that of the heat pulse propagating at a speed of 1.5 km/s. The heat pulse propagates at approximately the same speed as that in the theoretical prediction, whereas the turbulence pulse propagates one order of magnitude faster than that in the prediction, thereby providing important insights into the physics of non-local transport.

Improvement in multipass Thomson scattering system comprising laser amplification system developed in GAMMA 10/PDX.

The multipass Thomson scattering (MPTS) technique is one of the most useful methods for measuring low-electron-density plasmas. The MPTS system increases Thomson scattering (TS) signal intensities by integrating all multipass (MP) signals and improving the TS time resolution by analyzing each pass signal. The fully coaxial MPTS system developed in GAMMA 10/potential-control and diverter-simulator experiments has a polarization-based configuration with image-relaying optics. The MPTS system can enhance Thomson scattered signals for improving the measurement accuracy and megahertz-order time resolution. In this study, we develop a new MPTS system comprising a laser amplification system to obtain continuous MP signals. The laser amplification system can improve degraded laser power and return an amplified laser to the MP system. We obtain continuous MP signals from the laser amplification system by improving the laser beam profile adjuster in gas scattering experiments. Moreover, we demonstrate that more MP signals and stronger amplified MP signals can be achieved via multiple laser injections to the laser amplification system in the developed MP system comprising a laser amplification system.

Reformation of the Electron Internal Transport Barrier with the Appearance of a Magnetic Island.

When realising future fusion reactors, their stationary burning must be maintained and the heat flux to the divertor must be reduced. This essentially requires a stationary internal transport barrier (ITB) plasma with a fast control system. However, the time scale for determining the position of the foot point of an ITB is not clearly understood even though its understanding is indispensable for fast profile control. In this study, the foot point of the electron ITB (eITB) was observed to be reformed at the vicinity of a magnetic island when the island started to form. In addition, the enhanced confinement region was observed to expand during the eITB formation according to the radial movement of the magnetic island toward the outer region. Compared to the time scales of the local heat transport, the faster time scales of the movement of the eITB foot point immediately after island formation (~0.5 ms) suggest the importance of the magnetic island for plasma profile control to maintain stationary burning.

Coherence-imaging spectroscopy for 2D distribution of ion temperature and flow velocity in a laboratory magnetosphere.

A coherence-imaging spectroscopy (CIS) technique was developed to investigate plasma confinement in a dipole system that imitates a planetary magnetosphere. Optical interference generated using birefringent crystals enables two-dimensional Doppler spectroscopy to measure ion temperatures and flow velocities in plasmas. CIS covers the entire dynamics of the pole areas as well as of the core and edge areas on a dipole confinement device. The two-dimensional visualization of these quantities in the magnetospheric-plasma device RT-1 was demonstrated using CIS.

Development of a laser amplification system for the multi-pass Thomson scattering system for GAMMA 10/PDX.

The multi-pass Thomson scattering (MPTS) system is a useful technique for increasing the Thomson scattering (TS) signal intensities and improving the TS diagnostic time resolution. The MPTS system developed in GAMMA 10/PDX has a polarization-based configuration with an image relaying system. The MPTS system has been constructed for enhancing the Thomson scattered signals for the improvement of measurement accuracy and the megahertz sampling time resolution. However, in the normal MPTS system, the MPTS signal intensities decrease with the pass number because of the damping due to the optical components. Subsequently, we have developed a new MPTS system with the laser amplification system. The laser amplification system can improve the degraded laser power after six passes in the multi-pass system to the initial laser power. For the first time worldwide, we successfully obtained the continued multi-pass signals after the laser amplification system in the gas scattering experiments.

Nd:YAG laser Thomson scattering diagnostics for a laboratory magnetosphere.

A new Nd:YAG laser Thomson scattering (TS) system has been developed to explore the mechanism of high-beta plasma formation in the RT-1 device. The TS system is designed to measure electron temperatures (Te) from 10 eV to 50 keV and electron densities (ne) of more than 1.0 × 1017 m-3. To measure at the low-density limit, the receiving optics views the long scattering length (60 mm) using a bright optical system with both a large collection window (260-mm diameter) and large collection lenses (300-mm diameter, a solid angle of ∼68 × 10-3 str). The scattered light of the 1.2-J Nd:YAG laser (repetition frequency: 10 Hz) is detected with a scattering angle of 90° and is transferred via a set of lenses and an optical fiber bundle to a polychromator. After Raman scattering measurement for the optical alignment and an absolute calibration, we successfully measured Te = 72.2 eV and ne = 0.43 × 1016 m-3 for the coil-supported case and Te = 79.2 eV and ne = 1.28 × 1016 m-3 for the coil-levitated case near the inner edge in the magnetospheric plasmas.

Development of beam emission spectroscopy for turbulence transport study in Heliotron J.

This paper describes the development study of the beam emission spectroscopy (BES) for the turbulent transport study in Heliotron J. Modification of the sightlines (10 × 4 for edge and 10 × 2 for edge) enables us to obtain 2-dimensional BES imaging. The cooling effect on the reduction in the electrical noise of avalanche photodiode (APD) assembly has been investigated using a refrigerant cooling system. When the temperature of the APD element has set to be -20 °C, the electrical noise can be reduced more than 50%. The measurement error of the phase difference in the case of low signal level has been tested by two light-emitting diode lamps. The APD cooling has an effect to improve the measurement error at the low signal level of APD.

Calibrations of the LHD Thomson scattering system.

The Thomson scattering diagnostic systems are widely used for the measurements of absolute local electron temperatures and densities of fusion plasmas. In order to obtain accurate and reliable temperature and density data, careful calibrations of the system are required. We have tried several calibration methods since the second LHD experiment campaign in 1998. We summarize the current status of the calibration methods for the electron temperature and density measurements by the LHD Thomson scattering diagnostic system. Future plans are briefly discussed.

First measurement of time evolution of electron temperature profiles with Nd:YAG Thomson scattering system on Heliotron J.

A Nd:YAG Thomson scattering system has been developed for Heliotron J. The system consists of two 550 mJ 50 Hz lasers, large collection optics, and 25 radial channel (∼1 cm spatial resolution) interference polychromators. This measurement system achieves a S/N ratio of ∼50 for low-density plasma (ne ∼ 0.5 × 10(19) m(-3)). A time evolution of electron temperature profiles was measured with this system for a high-intensity gas-puff (HIGP) fueling neutral-beam-injection plasma. The peripheral temperature of the higher-density phase after HIGP recovers to the low-density pre-HIGP level, suggesting that improving particle transport in the HIGP plasma may be possible.

Highly time-resolved evaluation technique of instantaneous amplitude and phase difference using analytic signals for multi-channel diagnostics.

A fluctuation analysis technique using analytic signals is proposed. Analytic signals are suitable to characterize a single mode with time-dependent amplitude and frequency, such as an MHD mode observed in fusion plasmas since the technique can evaluate amplitude and frequency at a specific moment without limitations of temporal and frequency resolutions, which is problematic in Fourier-based analyses. Moreover, a concept of instantaneous phase difference is newly introduced, and error of the evaluated phase difference and its error reduction techniques using conditional/ensemble averaging are discussed. These techniques are applied to experimental data of the beam emission spectroscopic measurement in the Heliotron J device, which demonstrates that the technique can describe nonlinear evolution of MHD instabilities. This technique is widely applicable to other diagnostics having necessity to evaluate phase difference.

A novel electron density reconstruction method for asymmetrical toroidal plasmas.

A novel reconstruction method is developed for acquiring the electron density profile from multi-channel interferometric measurements of strongly asymmetrical toroidal plasmas. It is based on a regularization technique, and a generalized cross-validation function is used to optimize the regularization parameter with the aid of singular value decomposition. The feasibility of method could be testified by simulated measurements based on a magnetic configuration of the flexible helical-axis heliotron device, Heliotron J, which has an asymmetrical poloidal cross section. And the successful reconstruction makes possible to construct a multi-channel Far-infrared laser interferometry on this device. The advantages of this method are demonstrated by comparison with a conventional method. The factors which may affect the accuracy of the results are investigated, and an error analysis is carried out. Based on the obtained results, the proposed method is highly promising for accurately reconstructing the electron density in the asymmetrical toroidal plasma.

Improving the thermal stability of lactate oxidase by directed evolution.

Lactate oxidase is used in biosensors to measure the concentration of lactate in the blood and other body fluids. Increasing the thermostability of lactate oxidase can significantly prolong the lifetime of these biosensors. We have previously obtained a variant of lactate oxidase from Aerococcus viridans with two mutations (E160G/V198I) that is significantly more thermostable than the wild-type enzyme. Here we have attempted to further improve the thermostability of E160G/V198I lactate oxidase using directed evolution. We made a mutant lactate oxidase gene library by applying error-prone PCR and DNA shuffling, and screened for thermostable mutant lactate oxidase using a plate-based assay. After three rounds of screening we obtained a thermostable mutant lactate oxidase, which has six mutations (E160G/V198I/G36S/T103S/A232S/F277Y). The half-life of this lactate oxidase at 70 degrees C was about 2 times that of E160G/V198I and about 36 times that of the wild-type enzyme. The amino acid mutation process suggests that the combined neutral mutations are important in protein evolution.

The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders.

Mitochondria possess their own translational machinery, which is composed of components distinct from their cytoplasmic counterparts. To investigate the possible involvement of mitochondrial ribosomal defects in human disease, we mapped nuclear genes that encode mitochondrial ribosomal proteins (MRPs). We generated sequence-tagged sites (STSs) of individual MRP genes that were able to be detected by PCR. They were placed on an STS content map of the human genome by typing of radiation hybrid panels. We located 54 MRP genes on the STS-content map and assigned these genes to cytogenetic bands of the human chromosomes. Although mitochondria are thought to have originated from bacteria, in which the genes encoding ribosomal proteins are clustered into operons, the mapped MRP genes are widely dispersed throughout the genome, suggesting that transfer of each MRP gene to the nuclear genome occurred individually. We compared the assigned positions with candidate regions for mendelian disorders and found certain genes that might be involved in particular diseases. This map provides a basis for studying possible roles of MRP defects in mitochondrial disorders.

A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders.

Mapping of the human ribosomal protein (RP) genes has been completed, and all 80 different genes were placed on a cytogenetic map of the human genome. Because of the existence of processed pseudogenes, the localization of the RP genes was complicated, and five genes had remained to be mapped. Here we developed a novel strategy to identify sequence-tagged sites (STSs) at introns of the RP genes, and we localized RPL14, RPL22, RPL35, RPL36, and RPL39 within the chromosomes by radiation hybrid mapping. Unlike the case of eubacteria or archaebacteria, human RP genes are widely scattered about the genome. Together with the previous results, both sex chromosomes and 20 autosomes (all but chromosomes 7 and 21) were found to carry one or more RP genes. To explore the possible involvement of RP genes in human disorders, all 80 genes were assigned to cytogenetic bands according to a published cytogenetic BAC-STS map of the human genome. We compared the assigned positions with candidate regions for Mendelian disorders and found certain genes that might be involved in particular human disorders.

The human ribosomal protein L6 gene in a critical region for Noonan syndrome.

We have determined the genomic structure of the human ribosomal protein L6 gene (RPL6) and assigned it to the interval containing the Noonan syndrome locus. RPL6 spans 4415bp and consists of seven exons and six introns. The first exon is only 19bp in length, containing a 5' non-coding region and a polypyrimidine tract. The second exon starts with the initiator ATG. Although the overall structure of the protein is highly conserved among mammalian species, there is significant variation in the N-terminal portion. We have refined the position of RPL6, using two different radiation hybrid panels. RPL6 was mapped to chromosome 12q24.1 between the markers D12S84 and D12S861, which is in the critical region for Noonan syndrome.

Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome.

We have determined the organization and sequence of the region containing two ribosomal protein (rp) genes in the human and mouse genomes. The two genes, human RPL13A and RPS11, and mouse Rpl13a and Rps11, are tandemly located in both genomes with an interval of only 4.6kb in the case of the human genes and 1.6kb in the case of the mouse genes. The human RPL13A and RPS11 are 4236bp and 3254bp in length and comprise eight and five exons respectively, whereas the mouse Rps11 is 1951bp long and has five exons. Structural comparison of these genes, including previously reported mouse Rpl13a, revealed a significant conservation of sequences in the promoter regions. Although most rp genes are dispersed throughout the human genome, the conserved features and adjacent localization indicate possible coordinate transcription of the two genes. Furthermore, we have found that four small nucleolar RNA (snoRNA) genes are located in the introns of the two rp genes, both human and mouse. U32, U33, and U34 snoRNAs are encoded in introns 2, 4, and 5 of RPL13A respectively, and U35 in the sixth intron of RPL13A and the third intron of RPS11. The same organization of these snoRNA genes was also observed in the case of the mouse genes.

High-resolution mapping of ribosomal protein genes to human chromosome 19.

In a systematic effort for mapping of all the human ribosomal protein (rp) genes, we have found that an unusually large number (12) of rp genes are present on chromosome 19 and subsequently determined their locations on the chromosome by a radiation-hybrid procedure. For this, we isolated cosmid clones corresponding to each gene and placed nine of them on a metric physical map of chromosome 19. Although most genes are scattered over the chromosome, we found three genes are clustered in a 0.6-Mb region at 19q13.3 and two of them, RPL13A and RPS11, within a single cosmid only 4.3 kb apart. To explore a possible relationship between rp gene defects and human disease, we compared map positions of the rp genes and disease loci on chromosome 19, which led us to find RPS9 gene in the same interval as the gene for retinitis pigmentosa 11. The disease locus has previously been mapped to the 6-cM interval at 19q13.4 between markers D19S572 and D19S926, which corresponds to less than 2-Mb region on the metric physical map. We mapped RPS9 about 800 kb distal to D19S572.

A map of 75 human ribosomal protein genes.

We mapped 75 genes that collectively encode >90% of the proteins found in human ribosomes. Because localization of ribosomal protein genes (rp genes) is complicated by the existence of processed pseudogenes, multiple strategies were devised to identify PCR-detectable sequence-tagged sites (STSs) at introns. In some cases we exploited specific, pre-existing information about the intron/exon structure of a given human rp gene or its homolog in another vertebrate. When such information was unavailable, selection of PCR primer pairs was guided by general insights gleaned from analysis of all mammalian rp genes whose intron/exon structures have been published. For many genes, PCR amplification of introns was facilitated by use of YAC pool DNAs rather than total human genomic DNA as templates. We then assigned the rp gene STSs to individual human chromosomes by typing human-rodent hybrid cell lines. The genes were placed more precisely on the physical map of the human genome by typing of radiation hybrids or screening YAC libraries. Fifty-one previously unmapped rp genes were localized, and 24 previously reported rp gene localizations were confirmed, refined, or corrected. Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes. Chromosome 19, known to have a high gene density, contains an unusually large number of rp genes (12). This map provides a foundation for the study of the possible roles of ribosomal protein deficiencies in chromosomal and Mendelian disorders.