Transdisciplinary Research Integration Center

Minato-ku, Japan

Transdisciplinary Research Integration Center

Minato-ku, Japan
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Takada T.,National Institute of Genetics | Takada T.,Transdisciplinary Research Integration Center | Ebata T.,National Institute of Genetics | Noguchi H.,National Institute of Genetics | And 16 more authors.
Genome Research | Year: 2013

Commonly used classical inbred mouse strains have mosaic genomes with sequences from different subspecific origins. Their genomes are derived predominantly from the Western European subspecies Mus musculus domesticus, with the remaining sequences derived mostly from the Japanese subspecies Mus musculus molossinus. However, it remains unknown how this intersubspecific genome introgression occurred during the establishment of classical inbred strains. In this study, we resequenced the genomes of two M. m. molossinus-derived inbred strains, MSM/Ms and JF1/Ms. MSM/Ms originated from Japanese wild mice, and the ancestry of JF1/Ms was originally found in Europe and then transferred to Japan. We compared the characteristics of these sequences to those of the C57BL/6J reference sequence and the recent data sets from the resequencing of 17 inbred strains in the Mouse Genome Project (MGP), and the results unequivocally show that genome introgression from M. m. molossinus into M. m. domesticus provided the primary framework for the mosaic genomes of classical inbred strains. Furthermore, the genomes of C57BL/6J and other classical inbred strains have long consecutive segments with extremely high similarity (>99.998%) to the JF1/Ms strain. In the early 20th century, Japanese waltzing mice with a morphological phenotype resembling that of JF1/Ms mice were often crossed with European fancy mice for early studies of "Mendelism," which suggests that the ancestor of the extant JF1/Ms strain provided the origin of the M. m. molossinus genome in classical inbred strains and largely contributed to its intersubspecific genome diversity. © 2013, Published by Cold Spring Harbor Laboratory Press.

Segawa T.,Transdisciplinary Research Integration Center | Segawa T.,Japan National Institute of Polar Research | Takeuchi N.,Transdisciplinary Research Integration Center | Takeuchi N.,Chiba University
Annals of Glaciology | Year: 2010

Cyanobacterial communities on a glacier in the Qilian Shan, western China, were investigated using microscopic as well as 16S rRNA and internal transcribed spacer gene analyses. Microscopy revealed that there were abundant cyanobacteria on the entire glacier surface and their community consisted mainly of three morphological types. Low-cycle 16S rRNA gene sequences from six clone libraries were grouped into a total of eight cyanobacterial operational taxonomie units (OTUs), defined as 16S rRNA sequences with similarity of 99%. Although the cyanobacterial community based on morphological types displayed no significant differences among the study sites on the glacier, the community based on OTU groups varied among sites. This inconsistency may be due to simple morphology which might hide a large genetic variability. Phylogenetic analysis revealed that the OTU groups included the orders Oscillatoriales, Chroococcales and unclassified, and the majority of OTUs were Oscillatoriales. From the source environments of the cyanobacterial 16S rRNA gene sequences of each OTU on the glacier estimated by BLAST search (>97% similarity), 39.9% were from soil, 38.2% from fresh water and 1.7% from snow and ice environments. Based on geographical records in the database, all cyanobacterial OTUs were matched to those recorded from the Arctic and Antarctica. The results suggest that the cyanobacterial communities on the glacier are common in cold regions of the world and are likely not to be specialized members of the snow and ice biota but also inhabitants of soil and freshwater environments.

Segawa T.,Transdisciplinary Research Integration Center | Segawa T.,Japan National Institute of Polar Research | Takeuchi N.,Chiba University | Ushida K.,Kyoto Prefectural University | And 2 more authors.
Microbes and Environments | Year: 2010

To clarify altitudinal changes in the bacterial community on Gulkana Glacier in Alaska, we analyzed bacterial 16S rRNA gene by low-cycle PCR amplification, denaturing gradient gel electrophoresis (DGGE), and culturing in a snow-melt medium at 4°C. Low-cycle PCR-based cloning revealed the presence of 100 bacterial OTUs; however, 41 OTUs were identified only in a single clone, suggesting that their abundance was limited because of difficulty in predominating on the glacier. In contrast, 17 major OTUs accounted for 57-87% of the clone library at each site, suggesting that they accounted for the major part of the bacteria on the glacier. In addition, five of the 17 OTUs were included in the 21 OTUs cultured in the snowmelt medium. Based on the dominant phylotypes and DGGE results, the bacterial community on the glacier could be divided into three types, corresponding to the snow-covered, snow- and ice-covered, and bareice areas of the glacier. Our results suggest that a relatively limited number of bacteria predominate and that each phylotype is adapted to a distinct set of conditions on the glacier.

Nakazawa F.,Japan National Institute of Polar Research | Nakazawa F.,Transdisciplinary Research Integration Center | Konya K.,Japan Agency for Marine - Earth Science and Technology | Kadota T.,Japan Agency for Marine - Earth Science and Technology | Ohata T.,Japan Agency for Marine - Earth Science and Technology
Environmental Research Letters | Year: 2012

This study analyzed pollen in snow pits dug in September 2008 and September 2009 upstream of Potanin Glacier in the Mongolian Altai Mountains, which is a summer accumulation-type glacier, to investigate the environment for recent snow deposits. The snow pit observations in both years were carried out at sites 0 and 4, which are 3752 and 3890m above sea level, respectively. Seasonal layers of the pits were identified according to the taxon of pollen scattered during different seasons. In the 2007 and 2008 layers, concentration peaks of pollen taxa scattered from spring to summer were found at the same depth. Thus, the summer melt reached the spring layer such that pollen grains in the melted layer became concentrated on the summer melt surface and caused the pollen peaks. In contrast, the concentration peaks associated with each season appeared at different depths in the 2009 layer, suggesting that the degree of melting in 2009 was less than that in 2007 and 2008. This interpretation was supported by summer temperature data (June-August) for this region. Deviations in summer air temperatures from mean monthly temperatures for the summers of 1990-2009 were negative in 2009, whereas they were positive in 2007 and 2008. © 2012 IOP Publishing Ltd.

Himeno T.,Transdisciplinary Research Integration Center | Kanao M.,Japan National Institute of Polar Research | Ogata Y.,The Institute of Statistical Mathematics of Tokyo
Polar Science | Year: 2011

A large earthquake (Mw 8.1) that occurred off the North Coast of the Antarctic continent near the Balleny Islands on 25 March 1998 was the largest intra-plate earthquake ever recorded in the Antarctic Plate. The earthquake hypocenter catalog for this area shows a marked change in seismicity following the main shock in a large area around the Balleny aftershock region. However, the earthquake catalog includes many aftershocks and is affected by a variable detection rate. To overcome these limitations, we applied statistical models and methods, including Gutenberg-Richter's magnitude frequency distribution, the Epidemic-Type Aftershock Sequences (ETAS) model, and the space-time ETAS model, thereby enabling calculation of the change in detection rate. The results show a change in the spatial pattern of background seismicity over a large region after the 1998 event. © 2011 Elsevier B.V. and NIPR.

Oka A.,Transdisciplinary Research Integration Center | Shiroishi T.,Transdisciplinary Research Integration Center | Shiroishi T.,National Institute of Genetics
Genes and Genetic Systems | Year: 2014

Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation. © 2014, Genetics Society of Japan. All rights reserved.

Oka A.,Transdisciplinary Research Integration Center | Takada T.,Transdisciplinary Research Integration Center | Takada T.,National Institute of Genetics | Fujisawa H.,Transdisciplinary Research Integration Center | And 3 more authors.
PLoS Genetics | Year: 2014

Improper gene regulation is implicated in reproductive isolation, but its genetic and molecular bases are unknown. We previously reported that a mouse inter-subspecific X chromosome substitution strain shows reproductive isolation characterized by male-specific sterility due to disruption of meiotic entry in spermatogenesis. Here, we conducted comprehensive transcriptional profiling of the testicular cells of this strain by microarray. The results clearly revealed gross misregulation of gene expression in the substituted donor X chromosome. Such misregulation occurred prior to detectable spermatogenetic impairment, suggesting that it is a primal event in reproductive isolation. The misregulation of X-linked genes showed asymmetry; more genes were disproportionally downregulated rather than upregulated. Furthermore, this misregulation subsequently resulted in perturbation of global transcriptional regulation of autosomal genes, probably by cascading deleterious effects. Remarkably, this transcriptional misregulation was substantially restored by introduction of chromosome 1 from the same donor strain as the X chromosome. This finding implies that one of regulatory genes acting in trans for X-linked target genes is located on chromosome 1. This study collectively suggests that regulatory incompatibility is a major cause of reproductive isolation in the X chromosome substitution strain. © 2014 Oka et al.

Aoki K.,National Institute of Genetics | Nakajima R.,Transdisciplinary Research Integration Center | Furuya K.,National Institute of Genetics | Niki H.,National Institute of Genetics
Yeast | Year: 2010

Schizosaccharomyces japonicus is a fission yeast for which new genetic tools have recently been developed. Here, we report novel plasmid vectors with high transformation efficiency and an electroporation method for Sz. japonicus. We isolated 44 replicating segments from 12 166 transformants of Sz. japonicus genomic fragments and found a chromosomal fragment, RS1, as a new replicating sequence that conferred high transformation activity to Sz. japonicus cells. This sequence was cloned into a pUC19 vector with ura4+ of Sz. pombe (pSJU11) or the kan gene on the kanMX6 module (pSJK11) as selection markers. These plasmids transformed Sz. japonicus cells in the early-log phase by electroporation at a frequency of 123 cfu/μg for pSJK11 and 301 cfu/μg for pSJU11, which were higher than previously reported autonomously replicating sequences. Although a portion of plasmids remained in host cells by integration into the chromosome via RS1 segment, the plasmids could be recovered from transformants. The plasmid copy number was estimated to be 1.88 copies per cell by Southern blot analysis using a Sz. pombe ura4+ probe. The plasmid containing ade6+ suppressed the auxotrophic growth of the ade6-domE mutant, indicating that the plasmid would be useful for suppressor screening and complementation assays in Sz. japonicus. Furthermore, pSJU11 transformed Sz. pombe cells with the same frequency as the pREP2 plasmid. This study is a report to demonstrate practical use of episomal plasmid vectors for genetic research in Sz. japonicus. RS1 has been submitted to the DDBJ/EMBL/GenBank database (Accession No. AB547343). Copyright © 2010 John Wiley & Sons, Ltd.

Kagoshima H.,National Institute of Genetics | Kagoshima H.,Transdisciplinary Research Integration Center | Kohara Y.,National Institute of Genetics
Developmental Biology | Year: 2015

A wide variety of cells are generated by the expression of characteristic sets of genes, primarily those regulated by cell-specific transcription. To elucidate the mechanism regulating cell-specific gene expression in a highly specialized cell, AFD thermosensory neuron in Caenorhabditis elegans, we analyzed the promoter sequences of guanylyl cyclase genes, gcy-8 and gcy-18, exclusively expressed in AFD. In this study, we showed that AFD-specific expression of gcy-8 and gcy-18 requires the co-expression of homeodomain proteins, CEH-14/LHX3 and TTX-1/OTX1. We observed that mutation of ttx-1 or ceh-14 caused a reduction in the expression of gcy-8 and gcy-18 and that the expression was completely lost in double mutants. This synergy effect was also observed with other AFD marker genes, such as ntc-1, nlp-21and cng-3. Electrophoretic mobility shift assays revealed direct interaction of CEH-14 and TTX-1 proteins with gcy-8 and gcy-18 promoters in vitro. The binding sites of CEH-14 and TTX-1 proteins were confirmed to be essential for AFD-specific expression of gcy-8 and gcy-18 in vivo. We also demonstrated that forced expression of CEH-14 and TTX-1 in AWB chemosensory neurons induced ectopic expression of gcy-8 and gcy-18 reporters in this neuron. Finally, we showed that the regulation of gcy-8 and gcy-18 expression by ceh-14 and ttx-1 is evolutionally conserved in five Caenorhabditis species. Taken together, ceh-14 and ttx-1 expression determines the fate of AFD as terminal selector genes at the final step of cell specification. © 2015 Elsevier Inc.

Tanjo T.,Transdisciplinary Research Integration Center | Tamura N.,Kobe University | Banbara M.,Kobe University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

This paper describes a SAT-based CSP solver Azucar. Azucar solves a finite CSP by encoding it into a SAT instance using the compact order encoding and then solving the encoded SAT instance with an external SAT solver. In the compact order encoding, each integer variable is represented by using a numeral system of base B ≥ 2 and each digit is encoded by using the order encoding. Azucar is developed as a new version of an award-winning SAT-based CSP solver Sugar. Through some experiments, we confirmed Azucar can encode and solve very large domain sized CSP instances which Sugar can not encode, and shows better performance for Open-shop scheduling problems and the Cabinet problems of the CSP Solver Competition benchmark. © 2012 Springer-Verlag.

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