Genes & Genetic Systems
Online ISSN : 1880-5779
Print ISSN : 1341-7568
ISSN-L : 1341-7568
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GGS
  • 2020 Volume 95 Issue 2 Pages Cover-
    Published: April 01, 2020
    Released: July 08, 2020
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  • 2020 Volume 95 Issue 2 Pages Toc-
    Published: April 01, 2020
    Released: July 08, 2020
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  • 2020 Volume 95 Issue 2 Pages Index-
    Published: April 01, 2020
    Released: July 08, 2020
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Full papers
  • Chisa Mitsuhashi, Hiroshi Teramura, Hiroaki Shimada
    Type: Full paper
    2020 Volume 95 Issue 2 Pages 55-63
    Published: April 01, 2020
    Released: July 08, 2020
    [Advance publication] Released: April 18, 2020
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    Supplementary material

    In closed sea areas such as Tokyo Bay, a phenomenon known as a green tide often occurs, in which large amounts of Ulva seaweed grow abnormally and form mats along the coast. This is currently a serious environmental problem. Green tides are generated by the explosive growth of multiple types of Ulva algae. However, many Ulva species show similar characteristics to each other and are indistinguishable by appearance, making it difficult to identify the Ulva algae in green tides. In this study, we determined the entire nucleotide sequence of the chloroplast genome of Ulva pertusa (syn. Ulva australis) and identified two large inversions of gene order, suggesting the occurrence of genome inversions. We also detected structural polymorphisms among Ulva chloroplast genomes. Ulva pertusa was classified in a different clade from that containing U. lactuca and U. ohnoi, suggesting that U. pertusa is evolutionarily divergent from these species. Based on this knowledge, we constructed a genetic diagnosis system for Ulva algae. Using this approach, we established a simple method that can determine the species of Ulva algae by PCR using specific molecular markers, through which representative Ulva species such as U. lactuca, U. ohnoi and U. pertusa were easily distinguished.

  • Yuko Ukai, Komaki Inoue, Manaka Kamada, Hiroshi Teramura, Shunsuke Yan ...
    Type: Full paper
    2020 Volume 95 Issue 2 Pages 65-74
    Published: April 01, 2020
    Released: July 08, 2020
    [Advance publication] Released: May 09, 2020
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    Supplementary material

    Athyrium yokoscense shows strong tolerance to cadmium exposure, even at levels that are many times greater than the toxic levels in ordinary plants. To determine the mechanism of Cd tolerance in A. yokoscense, we grew these plants under high Cd conditions and observed the tissue-specific accumulation of Cd and generation of reactive oxygen species, which is one of the major physiological responses to Cd stress. Fuchsin staining indicated the existence of a casparian strip in A. yokoscense roots, which may participate in Cd hypertolerance in A. yokoscense. Moreover, we performed RNA-seq of RNA samples from A. yokoscense plants treated with or without Cd exposure and obtained comprehensive RNA sequences as well as the Cd-responsive expression patterns of individual genes. Through de novo transcriptome assembly and gene expression analysis, we found that A. yokoscense showed normal features with no significant change in the expression levels of any transporter genes, even under high Cd exposure conditions. Our results demonstrate that A. yokoscense has an unusual mechanism that allows the invading Cd to partition into the distal roots, thus avoiding translocation of Cd into the xylem.

  • Fumito Kanada, Yuhei Ogino, Toshiyuki Yoshida, Masaya Oki
    Type: Full paper
    2020 Volume 95 Issue 2 Pages 75-83
    Published: April 01, 2020
    Released: July 08, 2020
    [Advance publication] Released: April 03, 2020
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    Recent studies have revealed that tracking single cells using time-lapse fluorescence microscopy is an optimal tool for spatiotemporal evaluation of proteins of interest. Using this approach with Saccharomyces cerevisiae as a model organism, we previously found that heterochromatin regions involved in epigenetic regulation differ between individual cells. Determining the regularity of this phenomenon requires measurement of spatiotemporal epigenetic-dependent changes in protein levels across more than one generation. In past studies, we conducted these analyses manually to obtain a dendrogram, but this required more than 15 h, even for a single set of microscopic cell images. Thus, in this study, we developed a software-based analysis system to analyze time-lapse cellular images of S. cerevisiae, which allowed automatic generation of a dendrogram from a given set of time-lapse cell images. This approach is divided into two phases: a cell extraction and tracking phase, and an analysis phase. The cell extraction and tracking phase generates a set of necessary information for each cell, such as geometrical properties and the daughter–mother relationships, using image processing-based analysis techniques. Then, based on this information, the analysis phase allows generation of the final dendrogram by analyzing the fluorescent characteristics of each cell. The system is equipped with manual error correction to correct for the inevitable errors that occur in these analyses. The time required to obtain the final dendrograms was drastically reduced from 15 h in manual analysis to 0.8 h using this novel system.

  • Lan Anh Thi Le, Phooi Yee Chang, Sayaka Ando, Thomas M. Conrad, Shohei ...
    Type: Full paper
    2020 Volume 95 Issue 2 Pages 85-93
    Published: April 01, 2020
    Released: July 08, 2020
    [Advance publication] Released: May 11, 2020
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    Supplementary material

    Effects of environmental factors for growth of Escherichia coli on spontaneous mutagenesis and homologous recombination events are described. By analyzing rifampicin-resistant (Rifr) mutation frequencies in an E. coli strain lacking MutM and MutY repair enzymes, which suppress base substitution mutations caused by 8-oxoguanine (7,8 dihydro-8-oxoguanine; 8-oxoG) in DNA, we examined levels of oxidative DNA damage produced in normally growing cells. The level of 8-oxoG DNA damage was about 9- and 63-fold higher in cells grown in M9-glucose and M9-glycerol media, respectively, than in those grown in LB medium. We also found that about 14-fold more 8-oxoG DNA damage was produced in cells grown in about 0.1% oxygen than in those grown in the normal atmosphere. However, Rifr mutation frequency in wild-type cells was unchanged in such different growth conditions, suggesting that the capacity of repair mechanisms is sufficient to suppress mutations caused by 8-oxoG even at very high levels in cells growing in the particular conditions. On the other hand, the frequency of spontaneous homologous recombination events in wild-type E. coli cells varied with different growth conditions. When cells were grown in M9-glucose and M9-glycerol media, the spontaneous recombination frequency increased to about 4.3- and 7.3-fold, respectively, higher than that in LB medium. Likewise, the spontaneous recombination frequency was about 3.5-fold higher in cells growing in the hypoxic condition than in cells growing in the atmosphere. When cells were grown in anaerobic conditions, the recombination frequency decreased to half of that in the atmosphere. These data indicated that spontaneous homologous recombination is highly responsive to environmental factors such as nutrition and oxygen concentration.

Short communication
  • Shotaro Takenaka, Giri P. Joshi, Takashi R. Endo
    Type: Short communication
    2020 Volume 95 Issue 2 Pages 95-99
    Published: April 01, 2020
    Released: July 08, 2020
    [Advance publication] Released: March 16, 2020
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    Supplementary material

    Most deletions for the short arm of chromosome 2A (2AS), and the telocentric chromosome for the long arm of chromosome 2A (2AL), are available only in the heterozygous condition in ‘Chinese Spring’ hexaploid wheat. This is due to the female sterility, and therefore self-sterility, of their homozygotes, caused by the partial or entire loss of the 2AS chromosome arm on which genes for normal synapsis and female fertility are located. On the other hand, a D-genome disomic substitution line 2D(2A) of ‘Langdon’ tetraploid wheat, in which chromosome 2D is disomically substituted for chromosome 2A, is available (i.e., self-fertile) despite chromosome 2A being missing in this line. This fact indicates that another gene for female fertility must be present in Langdon 2D(2A). We attempted to develop self-fertile 2AS homozygous deletion and ditelosomic 2AL lines by transferring this female fertility gene, through a series of crosses and cytological screening, from Langdon 2D(2A) to the two aneuploid lines. We finally obtained self-fertile 2AS homozygous deletion and ditelosomic 2AL lines. These lines displayed normal meiotic chromosome pairing and lacked all 12 of the 2AS markers used for PCR analysis.

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