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  2. Shimada Makoto

Shimada Makoto

  (嶋田 誠)

Profile Information

Affiliation
Senior Assistant Professor, Institute for Comprehensive Medical Science, Fujita Health University
Cyukyo Gakuin University
Degree
Ph.D.(Kyoto University)
Researcher number
00528044
ORCID ID
 https://orcid.org/0000-0003-0067-0082
J-GLOBAL ID
200901081274695690
Researcher ID
K-4613-2015
researchmap Member ID
6000009803
External link
Bioinformaticsのアプローチを中心にスプライシングについて研究しています。
以前は、野生の霊長類の集団遺伝研究のため、のべ１年くらいアフリカでフィールド・ワークをしたこともあります。
その後、進化遺伝学、ゲノム進化、生物情報（転写物や多型データベースの研究）と幅を広げてきました。

Research Interests

 12

Research Areas

 7

Research History

 11
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Education

 3

Committee Memberships

 5

Awards

 1

Papers

 31
  • Shimada, Makoto K.
    International Journal of Molecular Sciences, 24(11) 9622, Jun 1, 2023  Peer-reviewedLead authorLast authorCorresponding author
  • Makoto K. Shimada, Tsunetoshi Nishida
    MOLECULAR PHYLOGENETICS AND EVOLUTION, 109 409-414, Apr, 2017  Peer-reviewedLead authorCorresponding author
    Felsenstein's PHYLIP package of molecular phylogeny tools has been used globally since 1980. The programs are receiving renewed attention because of their character-based user interface, which has the advantage of being scriptable for use with large-scale data studies based on super-computers or massively parallel computing clusters. However, occasionally we found, the PHYLIP Consense program output text file displays two or more divided bootstrap values for the same cluster in its result table, and when this happens the output Newick tree file incorrectly assigns only the last value to that cluster that disturbs correct estimation of a consensus tree. We ascertained the cause of this aberrant behavior in the bootstrapping calculation. Our rewrite of the Consense program source code outputs bootstrap values, without redundancy, in its result table, and a Newick tree file with appropriate, corresponding bootstrap values. Furthermore, we developed an add-on program and shell script, add_bootstrap.pl and fasta2tre_bs.bsh, to generate a Newick tree containing the topology and branch lengths inferred from the original data along with valid bootstrap values, and to actualize the automated inference of a phylogenetic tree containing the originally inferred topology and branch lengths with bootstrap values, from multiple unaligned sequences, respectively. These programs can be downloaded at: https://github.com/ShimadaMK/PHYLIP_enhance/. (C) 2017 Elsevier Inc. All rights reserved.
  • Makoto K. Shimada, Ryoko Sanbonmatsu, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Yoshiyuki Suzuki, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi
    MOLECULAR GENETICS AND GENOMICS, 291(5) 1851-1869, Oct, 2016  Peer-reviewedLead authorCorresponding author
    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases.
  • Makoto K. Shimada, Noriko Sasaki-Haraguchi, Akila Mayeda
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16(5) 10376-10388, May, 2015  Peer-reviewedLead author
    According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37-65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism.
  • Shimada, Makoto
    Research Bulletin, Saito Ho-on Kai Museum, 78 77-85, Mar, 2014  InvitedLead authorCorresponding author
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Misc.

 27
  • Makoto SHIMADA
    Primate Research, 40(1), Jun 20, 2024  InvitedLead authorCorresponding author
  • 嶋田 誠
    岩波『科学』, 91(2) 178-181, Feb, 2021  InvitedLead authorCorresponding author
  • Y SUGIYAMA, K MATSUBAYASHI, T SHOTAKE, Y KAWAMOTO, M SHIMADA
    Primate Research, 36(2) 67-72, Dec 20, 2020  
  • Makoto K. Shimada, Tsunetoshi Nishida
    bioRxiv, Mar 29, 2020  
    <title>Abstract</title>The application of current genome-wide sequencing techniques on human populations helps elucidate the considerable gene flow among genus<italic>Homo</italic>, which includes modern and archaic humans. Gene flow among current human populations has been studied using frequencies of single nucleotide polymorphisms. Unlike single nucleotide polymorphism frequency data, haplotype data are suitable for identifying and tracing rare evolutionary events. Haplotype data can also conveniently detect genomic location and estimate molecular function that may be a target of selection. We analyzed eight loci of the human genome using the same procedure for each locus to infer human haplotype diversity and reevaluate past explanations of the evolutionary mechanisms that affected these loci. These loci have been recognized by separate studies because of their unusual gene genealogy and geographic distributions that are inconsistent with the recent out-of-Africa model. For each locus, we constructed genealogies for haplotypes using sequence data of the 1000 Genomes Project. Then, we performed S* analysis to estimate distinct gene flow events other than out-of-Africa events. Furthermore, we also estimated unevenness of selective pressure between haplotypes by Extended Haplotype Homozygosity analysis. Based on the patterns of results obtained by this combination of analyses, we classified the examined loci without using a specific population model. This simple method helped clarify evolutionary events for each locus, including rare evolutionary events such as introgression, incomplete lineage sorting, selection, and haplotype recombination that may be hard to discriminate from each other.
  • Makoto K. Shimada
    GENES & GENETIC SYSTEMS, 91(6) 343-343, Dec, 2016  
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Books and Other Publications

 2
  • (Role: Contributor, Chap. 2, The Genons, The Baboons)
    Maruzen Publishing, Jul, 2023 (ISBN: 9784621308042)
  • Shimada, Makoto (Ediotrs, Matsuzawa, Tetsuro, Humle, Tatyana, Sugiyama, Yukimaru, Tetsuro Matsuzawa, Tatyana Humle, Yukimaru Sugiyama (Role: Joint author, Chap. 34, pp339-345, Genetic variation in the chimpanzees of Bossou and Nimba.; Append. E, DNA sequencing data, pp416-419)
    Springer, Jun, 2011 (ISBN: 4431539204)

Presentations

 12
  • 嶋田 誠
    生涯学習推進講座「知を立てる講座」, Sep 10, 2023, 知立市生涯学習スポーツ課  Invited
  • 嶋田誠
    第75回インシリコ・メガバンク研究会, Sep 2, 2016, 東北大学東北メディカル・メガバンク機構 ゲノム解析部門 バイオメディカル情報解析分野  Invited
    数塩基の短い塩基配列の反復である、STR (Short Tandem Repeat) は反復数変化が高頻度に起こる。そこで反復数の高変異性を通じて、適応的形質や進化的安定状態を速やかに獲得したとする仮説が提唱されている。反面、ヒトの反復配列には、神経変性疾患の原因となる反復配列が複数知られている。そのような危険な複数の反復配列がなぜ人類集団に維持されているのか、良くわかっていない。我々は自分たちが構築し公開している、遺伝子データベース、H-invDBに多型情報を統合することで、ヒトゲノム中のSTR反復数および反復多型状態を決定した。さらに相互比較することによって、それぞれのSTRにおける選択圧を評価した。その結果、アミノ酸コード領域中STRにはプロリン反復とグルタミン反復をそれぞれ代表例とする二つの機構により、DNA配列レベルで反復を短く抑えながらも、反復アミノ酸配列を実現していることが分かった。さらにグルタミン反復はアミノ酸レベルで長い反復を持つ傾向があり、特に反復多型座位は、脳・神経系の発生調節に関わる遺伝子中に存在する傾向が明らかになった。我々の結果は、これらの反復座位が多型を持つことで脳・神経系の発生調節に関する機能の多様化を促した可能性を示した。さらに、人類進化における社会性の進化とSTRの神経発達調節におけるスイッチ機能の関連を議論したい。
  • 嶋田誠
    武蔵野大学 人間科学研究所シンポジウム 知性はどこから来たか - こころの進化と遺伝 -, Dec 4, 2015, 武蔵野大学 人間科学研究所  Invited
  • 嶋田 誠
    7th Cafe （名古屋市中区栄・ナディアパーク7階）, Jul 18, 2014  Invited
  • 嶋田誠
    第102回システム自然科学研究科セミナー, May 19, 2014, 名古屋市立大学システム自然科学研究科  Invited
  • Shimada, Makoto
    Jan 12, 2013, Replacement of Neanderthals by Modern Humans (RNMH): Testing Evolutionary Models of Learning
  • Shimada, Makoto
    International Conference on Replacement of Neanderthals by Modern Humans: Testing Evolutionary Models of Learning (RNMH2012), Nov 18, 2012
  • Shimada MK, Sasaki-Haraguchi N, Mayeda A
    Annual Meeting of the Society for Molecular Biology and Evolution (SMBE2011), Jul, 2011
  • Shimada MK, Sasaki-Haraguchi N, Mayeda A
    The 16th Annual Meeting of the RNA Society and The RNA Society of Japan 13th Annual Meeting, Jun, 2011
    Kyoto, Japan. Program & Abstracts (Oral Abstracts) #41
  • Shimada MK
    Symposium on Biodiversity Sciences, “Genome, Evolution and Environment” (ISBDS2010: Commemorating the 60th Anniversary of Nagoya City University & in Partnership with the 10th Conference of the Parties to the Convention of Biological Diversity, CBD-COP10), Aug 1, 2010, Graduate School of Natural Sciences, Nagoya City University  Invited
    Decrease of natural forests have been accelerated by development of human activity, which leads to loss of biodiversity. Populations of great apes are vulnerable to forest loss because of their low fecundity and their high dependency on forests for their habitat. What forest fragmentation will bring about to wild ape populations is becoming more important question. The wild chimpanzee (Pan troglodytes verus) community in the Bossou, Republic of Guinea, whose core area is restricted to approximately 6 km2 by human activity, with a size of approximately 20 members, is one of the smallest chimpanzee communities among long-term studied communities. There are a few neighboring chimpanzee community in the Nimba mountain area, however the Bossou community has no evidence of contact with neighboring populations, and no female immigration after initiation of observation in 1976. We collected samples of chimpanzees non-invasively from the Bossou and Nimba mountain areas, and sequenced 605 bp from the most variable region in mitochondrial DNA (mtDNA), to reveal maternal genetic relationship among all individuals of Bossou community and to infer their breeding history and mating strategy. We found the followings: 1) no clear population structure emerged as in other populations of West African chimpanzee (P. t. verus), suggesting that gene flow was sufficient in the common ancestral population of West African chimpanzees; 2) there is no matrilineal gene exchange between Bossou and Nimba chimpanzees among the current generations; 3) 4 of the 8 original adult members of the Bossou community are likely matrilineal relatives, which results in a skewed frequency of one mtDNA haplotype occupying about 50%; 4) so far, the matrilineal genetic diversity of the Bossou community is still relatively stable, but there is a high risk of haplotype extinction due to a skewed haplotype distribution and a predicted relaxation of incest avoidance; 5) finally, hair samples showed an inferior result to other sample types, such as urine, feces, and wadges (chewed up fruit remains).
  • Shimada MK, Hey J
    The 74th Annual Meeting of American Association of Physical Anthropologists., Apr, 2005
    Culotta, E: Archaic Gene in Modern People? (News) Science 308: 490-491, 22 April 2005. http://www.sciencemag.org/content/308/5721/490.2.full
  • 嶋田誠
    日本ナイル・エチオピア学会 第８回学術大会, Jul 3, 1999

Teaching Experience

 10
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Professional Memberships

 7
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Works

 2

Research Projects

 13
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Academic Activities

 29
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Social Activities

 7

Media Coverage

 2
  • 中日新聞社, 中日新聞 夕刊, Jan 11, 2014 Newspaper, magazine
    文部科学省科研費 新学術領域（新学術領域「交代劇」・公募研究）研究紹介
  • AAAS, Science (News), Science 308: 490-491, 22 April 2005, Apr 22, 2005 Promotional material
    Report and Interview about my presentation at The 74th Annual Meeting of American Association of Physical Anthropologists.

Other

 14
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教育内容・方法の工夫（授業評価等を含む）

 2
  • 件名（英語）
    藤田保健衛生大学内Faculty Development講習受講
    開始年月日（英語）
    2012/08/07
    終了年月日（英語）
    2012/08/07
    概要（英語）
    「ティーチング・ポートフォリオTPの導入･活用の実際と課題」
    外部講師： 土持ゲーリー法一
    （帝京大学高等教育開発センター長 ファカルティ・ディベロッパー
  • 件名（英語）
    第１回藤田保健衛生大学医学部医学情報教育ワークショップ「eラーニングシステムを体験する―Moodleの基礎―」修了
    開始年月日（英語）
    2014/06/24
    終了年月日（英語）
    2014/07/08

作成した教科書、教材、参考書

 1
  • 件名（英語）
    大学院特別講義資料（Web公開）
    開始年月日（英語）
    2012/10/09
    概要（英語）
    名古屋大学医学研究科での大学院特別講義資料を以下にて公開している。
    http://tinyurl.com/shimada-mk/

その他教育活動上特記すべき事項

 3
  • 件名（英語）
    Member of the Medical Science Cafe Committee in Assembly II activity
    開始年月日（英語）
    2017/04/01
    概要（英語）
    総合医科学研究所主催第2回メディカル・サイエンス・カフェの実行委員として学内アセンブリII（プロジェクト代表：倉橋総医研所長）活動を指導した。
  • 件名（英語）
    Staff of Soccer Group in Assembly I activitiy
    開始年月日（英語）
    2009/05/11
    概要（英語）
    学内アセンブリ教育(各学部・学校1年時)サッカー班
  • 件名（英語）
    Academic adviser of senior thesis
    開始年月日（英語）
    2018/04/02
    終了年月日（英語）
    2018/10/15
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