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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.

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.

Sugimoto H.,National Institute of Genetics | Sugimoto H.,Transdisciplinary Research Integration Center | Okabe S.,Azabu University | Kato M.,Kato Acoustics Consulting Office | And 7 more authors.
PLoS ONE | Year: 2011

Male mice emit ultrasonic vocalizations (USVs) towards females during male-female interaction. It has been reported that USVs of adult male mice have the capability of attracting females. Although the waveform pattern of USVs is affected by genetic background, differences among strains with respect to USV and the effects of these differences on courtship behavior have not been analyzed fully. We analyzed USV patterns, as well as actual social behavior during USV recording, in 13 inbred mouse strains, which included laboratory and wild-derived strains. Significant effects of strain were observed for the frequency of USV emission, duration, and frequency of the waveform category. Principal component (PC) analysis showed that PC1 was related to frequency and duration, and PC2-4 were related to each waveform. In the comparison of USV patterns and behaviors among strains, wild-derived KJR mice displayed the highest scores for PC2-4, and female mice paired with KJR males did not emit rejection-related click sounds. It is assumed that the waveforms emitted by KJR males have a positive effect in male-female interaction. Therefore, we extracted waveforms in PC2-4 from the USV recordings of KJR mice to produce a sound file, "HIGH2-4". As a negative control, another sound file ("LOW2-4") was created by extracting waveforms in PC2-4 from strains with low scores for these components. In the playback experiments using these sound files, female mice were attracted to the speaker that played HIGH2-4 but not the speaker that played LOW2-4. These results highlight the role of strain differences in the waveforms of male USVs during male-female interaction. The results indicated that female mice use male USVs as information when selecting a suitable mate. © 2011 Sugimoto 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.

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