26 Works

Additional file 2 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 2: Table S1. List of DEG candidates identified by comparative transcriptome analysis of c versus i/p cells from stage-3 embryo (comparison I). Table S2. List of DEG candidates identified by comparative transcriptome analysis of p versus c/i cells from stage-3 embryo (comparison II). Table S3. List of DEG candidates identified by comparative transcriptome analysis of i versus c/p cells from stage-3 embryo (comparison III). Table S4. List of DEG candidates indentified by comparative...

Additional file 9 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 9: Table S9. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 2. Table S10. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 3. Table S11. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at early stage 5.

Additional file 11 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 11: Table S14. Data from comparative analysis of read counts in extracted ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 using edgeR. Table S15. List of differential ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 (FDR < 0.05).

Additional file 14 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 14. Multi-fasta format file of 118 sequences (75 amino acid sites) used for the first ML analysis.

Additional file 15 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 15. Multi-fasta format file of 168 sequences (63 amino acid sites) used for the second ML analysis.

Data from: Infants prefer the faces of strangers or mothers to morphed faces: an uncanny valley between social novelty and familiarity

Yoshi-Taka Matsuda, Yoko Okamoto, Misako Ida, Kazuo Okanoya, Masako Myowa-Yamakoshi & Y.-T. Matsuda
The “uncanny valley” response is a phenomenon involving the elicitation of a negative feeling and subsequent avoidant behaviour in human adults and infants as a result of viewing very realistic humanlike robots or computer avatars. It is hypothesised that this uncanny feeling occurs because the realistic synthetic characters elicit the concept of “human” but fail to satisfy it. Such violations of our normal expectations regarding social signals generate a feeling of unease. This conflict-induced uncanny...

Data from: Learning of efficient behaviour in spatial exploration through observation of behaviour of conspecific in laboratory rats

Yuji Takano, Masatoshi Ukezono, Satoshi F. Nakashima, Nobuaki Takahashi & Naoyuki Hironaka
Recent studies have suggested that rodent behaviour is influenced by the behaviour of surrounding conspecifics (e.g. emotional contagion and prosocial behaviour). However, little is known about deferred imitation and complex observational learning in rats. The purpose of this study was to reveal whether rats can learn from another rat's experiences. In a maze, observer rats watched the foraging behaviour of other rats (demonstrators) and then foraged in turn. The results showed that demonstrators explored inefficiently,...

Data from: Genotype-aggregated planting improves yield in Jerusalem artichoke (Helianthus tuberosus) due to self/non-self discrimination

Yuya Fukano, Wei Guo, Koji Noshita, Shoko Hashida & Shotaka Kamikawa
Accumulating evidence indicates that plants are capable of self/non-self and kin/stranger discrimination. Plants increase biomass of and resource allocation to roots when they encounter roots of conspecific non-self neighbors, but not when they encounter self roots. Root proliferation usually occurs at the expense of reproductive investment. Therefore, if clonal crops are capable of self/non-self discrimination, spatially aggregated planting with seedlings of the same genotype may decrease root proliferation and produce a higher yield than planting...

Additional file 12 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 12: Table S16. Primers and cDNA clones used for RNAi and in situ hybridization.

Additional file 13 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 13. Multi-fasta format file of 212 protein sequences used for molecular phylogenetic characterization.

Additional file 2 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 2: Table S1. List of DEG candidates identified by comparative transcriptome analysis of c versus i/p cells from stage-3 embryo (comparison I). Table S2. List of DEG candidates identified by comparative transcriptome analysis of p versus c/i cells from stage-3 embryo (comparison II). Table S3. List of DEG candidates identified by comparative transcriptome analysis of i versus c/p cells from stage-3 embryo (comparison III). Table S4. List of DEG candidates indentified by comparative...

Additional file 9 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 9: Table S9. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 2. Table S10. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at stage 3. Table S11. List of DEGs identified by comparative transcriptome analysis of fuchi pRNAi versus untreated embryos at early stage 5.

Additional file 5 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 5: Movie S2. Time-lapse video showing phenotypes gfp, g26874, g7720, and g4238 pRNAi embryos. Time after egg laying (AEL) and time after start of recording are indicated. Movie starts are adjusted by the timing of blastoderm formation. Some of the embryos are the same as those shown in Fig. 3A. Scale bar, 100 µm.

Additional file 5 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 5: Movie S2. Time-lapse video showing phenotypes gfp, g26874, g7720, and g4238 pRNAi embryos. Time after egg laying (AEL) and time after start of recording are indicated. Movie starts are adjusted by the timing of blastoderm formation. Some of the embryos are the same as those shown in Fig. 3A. Scale bar, 100 µm.

Additional file 7 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 7: Table S7. List of bioinformatic resources used for phylogenetic characterization of Fuchi and other GATA family members in spiders. Table S8. Amino acid sequence alignment and classification of GATA family members from spiders and other metazoans.

Additional file 10 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 10: Table S12. Data from comparative analysis of read counts in extracted ATAC-seq peaks between fuchi pRNAi and wild-type embryos at stage 3 using edgeR. Table 13. List of differential ATAC-seq peaks between fuchi pRNAi and wild-type embryos at stage 3 (FDR < 0.05).

Additional file 12 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 12: Table S16. Primers and cDNA clones used for RNAi and in situ hybridization.

Additional file 13 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 13. Multi-fasta format file of 212 protein sequences used for molecular phylogenetic characterization.

New Ultrahigh Affinity Host−Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations

Sarvin Moghaddam, Cheng Yang, Mikhail Rekharsky, Young Ho Ko, Kimoon Kim, Yoshihisa Inoue & Michael K. Gilson
A dicationic ferrocene derivative has previously been shown to bind cucurbit[7]uril (CB[7]) in water with ultrahigh affinity (ΔGo = −21 kcal/mol). Here, we describe new compounds that bind aqueous CB[7] equally well, validating our prior suggestion that they, too, would be ultrahigh affinity CB[7] guests. The present guests, which are based upon either a bicyclo[2.2.2]octane or adamantane core, have no metal atoms, so these results also confirm that the remarkably high affinities of the ferrocene-based...

Data from: Rewiring of embryonic glucose metabolism via suppression of pfk-1/aldolase during mouse chorioallantoic branching

Hidenobu Miyazawa, Yoshifumi Yamaguchi, Yuki Sugiura, Kurara Honda, Koki Kondo, F. Matsuda, Takehiro Yamamoto & Makoto Suematsu
Adapting the energy metabolism state to changing bioenergetic demands is essential for mammalian development accompanying massive cell proliferation and cell differentiation. However, it remains unclear how developing embryos meet the changing bioenergetic demands during the chorioallantoic branching (CB) stage when the maternal-fetal exchange of gases and nutrients is promoted. In this study, using metabolome analysis with mass-labeled glucose, we found that developing embryos redirected glucose carbon flow into the pentose phosphate pathway (PPP) via suppression...

Additional file 10 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 10: Table S12. Data from comparative analysis of read counts in extracted ATAC-seq peaks between fuchi pRNAi and wild-type embryos at stage 3 using edgeR. Table 13. List of differential ATAC-seq peaks between fuchi pRNAi and wild-type embryos at stage 3 (FDR < 0.05).

Additional file 11 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 11: Table S14. Data from comparative analysis of read counts in extracted ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 using edgeR. Table S15. List of differential ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 (FDR < 0.05).

Additional file 14 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 14. Multi-fasta format file of 118 sequences (75 amino acid sites) used for the first ML analysis.

Additional file 15 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 15. Multi-fasta format file of 168 sequences (63 amino acid sites) used for the second ML analysis.

Additional file 7 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Sawa Iwasaki-Yokozawa, Ryota Nanjo, Yasuko Akiyama-Oda & Hiroki Oda
Additional file 7: Table S7. List of bioinformatic resources used for phylogenetic characterization of Fuchi and other GATA family members in spiders. Table S8. Amino acid sequence alignment and classification of GATA family members from spiders and other metazoans.

Registration Year

  • 2022
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    2
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  • 2012
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Resource Types

  • Dataset
    26

Affiliations

  • Japan Science and Technology Agency
    26
  • Osaka University
    21
  • Japan Tobacco (Japan)
    20
  • Doshisha University
    2
  • University of Tokyo
    2
  • Institute for Basic Science
    1
  • Keio University
    1
  • Kwansei Gakuin University
    1
  • University of Maryland, College Park
    1