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Tree-thinkers Lab✨分子生命史研究室

@kurakulabmsm.bsky.social
291 followers 151 following 43 posts

Molecular Life History Lab led by Shigehiro Kuraku at National Institute of Genetics in Mishima, Japan. Home of Squalomix & MedakaBase フィールド&分子生物学実験寄り動物ゲノム情報学&分子進化学研究とリテラシー普及@遺伝研

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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 02/10/2026
[Our blog] Gecko as a reptilian model - another long-term focus that shaped our scope. www.treethinkers.info/en/post/geck... delivered from Molecular Life History Laboratory (Kuraku Lab) at National Institute of Genetics, in Mishima, Japan.
treethinkers.info
Gecko as reptilian 'model'
Since the era before our lab got its current shape at NIG in Mishima, one of our interests has been tracing vertebrate genome evolution. To facilitate unbiased comparisons, we have also worked on gene...
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 13/09/2026
Our study on the whale shark visual pigment published earlier in PNAS www.pnas.org/doi/10.1073/... will be presented this week in Siena, Italy, at 21th Intl Conf Retinal Proteins #ICRP2026 #ICRP #CSNB #Squalomix
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ECCB 2026 @eccb26leiden.bsky.social · 05/01/2026
A great start to the new year: registration for the European Congress of Conservation Biology (ECCB 2026) is now officially open! Participants can take advantage of a special Early Bird discount, available until 31 March 2026. More on: eccb26leiden.eu/registration/
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 12/02/2026
Huge congrats to Sean & Tatiana on their new @cp-iscience.bsky.social paper! doi.org/10.1016/j.is... Tracing the Kazald quartet from sharks to tetrapods—a fantastic milestone for Sean’s PhD journey in Europe. @squalomix4earth.bsky.social pride ! 🦈🧬
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 12/02/2026
ここから来年度への研究室の外向き(国内)発信のラフな予定です 3月2日 メダカの会でゲノム情報リソース紹介 3月31日 ワークショップ「生命の樹」を主催(まだ参加受付中) 4月 大学院説明会にて研究室紹介 開催日未定 研究会「自然と社会を読み解く分子進化学のフロンティア」を主催 開催日未定 研究会「生命科学を支える分子系統学 2026」を主催
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OneZoom @onezoom.bsky.social · 28/07/2025
What on earth is a 'fish'? Inspired by @hankgreen.bsky.social's video 'Sharks Aren't Fish' we've put together this link where you can explore the bony vertebrates on OneZoom (in turquoise), as well as some of his standout examples of thats-not-really-a-fish (in red) www.onezoom.org/life/@Chorda...
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IreneJulca @irenejulca.bsky.social · 18/11/2025
Interested in the newest developments in orthology? Check out the last Quest for Orthologs (QfO9) meeting report: link.springer.com/article/10.1... #orthology #function #domains #AI #paralogy Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.
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Shawn Burgess @burgesslab.bsky.social · 17/11/2025
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv: www.biorxiv.org/content/10.1...
biorxiv.org
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7th World Conference on Marine Biodiversity @wcmb2026.bsky.social · 17/11/2025
REGISTRATION IS NOW OPEN!! Start your countdown; #WCMB2026 is happening exactly one year from now! Register here: wcmb2026.org/registration @unoceandecade.bsky.social @vliz.be #marinebiodiversity
wcmb2026.org
Register here
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国立遺伝学研究所 @nigidenken.bsky.social · 27/10/2025
国立遺伝学研究所は、遺伝形質研究系教授または准教授を公募します。2025年12月24日(水)正午必着。採用条件は微生物あるいは微生物に関連した生命現象を対象とする研究分野で優れた業績を持ち、遺伝研核生物リソースを発展させられること。ご応募お待ちしています。募集要項 www.nig.ac.jp/nig/ja/2025/...
nig.ac.jp
遺伝形質研究系 教授又は准教授 公募 応募締切:2025年12月24日(水)正午必着 | 国立遺伝学研究所
遺伝学の中核拠点として生命システムの解明を目指す先端研究や共同利用・共同研究を推進しています。また、総研大 先端学術院 遺伝学コースを併設し大学院教育を行っています。
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Molecular Biology and Evolution @molbioevol.bsky.social · 13/10/2025
Lagman, Bergqvist & Kuraku analysed opsin gene evolution in jawless vertebrates, confirming tandem duplications of visual opsins before the vertebrate radiation. 🔗 doi.org/10.1093/molbev/msaf231 #evobio #molbio #opsins
doi.org
Tandem Gene Clusters as Phylogenetic Anchors Reveal the Hidden History of Vertebrate Visual Opsins
Abstract. The expansion of the visual opsin gene family was a crucial event in the diversification of vertebrate vision in evolution. Additional expansions
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Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 04/09/2025
Thanks to our whole EBP community for making this milestone possible. | @bat1kgenomes.bsky.social | @kurakulabmsm.bsky.social | @atlasea.bsky.social | @biogeneurope.bsky.social | @ergabiodiv.bsky.social | @vertebrategenomes.bsky.social | @invertebrates.bsky.social | @projectpsyche.bsky.social |
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 06/09/2025
​Due to a power outage caused by a lightning strike on Sep 5th, the web servers operated by us, incl. #aLeaves (but excl. #gVolante), are currently down. More information could be posted at the top of this 'annex' page (which is still alive) if the down time lasts long. github.com/Squalomix/me...
github.com
GitHub - Squalomix/medaka-annex: Listing of omics data resources for medaka fishes coordinated by Medaka Informatics Team of Japan's National BioResource Project (NBRP), namely Kuraku Lab at National ...
Listing of omics data resources for medaka fishes coordinated by Medaka Informatics Team of Japan's National BioResource Project (NBRP), namely Kuraku Lab at National Institute of Genetics in M...
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 31/08/2025
Travelling back from Intl Basking Shark Conf in Galway, Ireland. It's so important for those studying the species that travels across oceans to connect globally. Huge thanks to everyone who worked hard to make the conf happen. Love to visit 🇮🇪 again!! #Squalomix
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Dfam Database of Transposable Elements @dfam.bsky.social · 06/08/2025
Today we’re introducing a major update to the family seed alignments, protein features, and relationship data visualizations on the Dfam website. In addition, we are adding two new datasets: ULTRA reported tandem repeats, and self-alignments.
xfam.wordpress.com
Dfam Family Visualization Improvements
Today we’re introducing a major update to how TE family seed alignments, protein features, and relationship data are visualized on the Dfam website. Previously, these datasets were presented separa…
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日経サイエンス @nikkei-science.com · 26/08/2025
「野生生物を虐げる不法ペット貿易」 自然界から生物が姿を消しているのは,生息地の喪失よりも野生動物のペット取引によるところが大きいかもしれない。 別冊日経サイエンス274『鳥の惑星 飛翔, 渡り, さえずりを科学する』 www.nikkei-science.com/sci_book/bes...
nikkei-science.com
鳥の惑星 飛翔, 渡り, さえずりを科学する|日経サイエンス
まえがき 第1章 鳥の飛翔と渡り 羽毛の進化 自然が育んだ鳥の機能美  M. B. ハビブ 渡り鳥の量子コンパス 高精度ナビの仕組み  P. J. ホア/ H. モウリットセン 動物たちの磁気感覚  出村政彬 第2章 鳥 … 続きを読む →
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 18/08/2025
Confirmed the ties between consortia @ergabiodiv.bsky.social and #Squalomix by visiting at the ERGA booth with @rmwaterhouse.bsky.social at #ESEB2025
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 23/07/2025
New chapter of sex determination, with sharks and rays! Our study, utilizing embryonic samples from cooperative aquariums, revealed the ancient sex chromosome origin and unique sex determination potentials. Published today in PNAS www.pnas.org/doi/full/10.... #Squalomix
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 10/07/2025
www.science.org/content/arti...
science.org
Mutation behind night blindness in humans helps whale sharks see in the dark
Alterations in vision gene allow massive fish to detect blue light in inky depths
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 10/07/2025
www.haaretz.com/science-and-...
haaretz.com
Obesity genes evolved 450 million years ago, shark study reveals
***
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国立遺伝学研究所 @nigidenken.bsky.social · 04/07/2025
\ ⏰まだまだ参加募集中 / 三島市内小学生のみなさま、遺伝研でお待ちしています!!
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 01/07/2025
Very curious to follow up how the taxa of our interests, particularly Chondrichthyes 🦈, of course, are catalogued under this 'Tree of Sex Consortium' relaunched.
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 15/06/2025
Ready for Satellite Symposium at Okinawa Churaumi Aquarium, our long-term scientific partner, after fruitful days at #ipfc12 in Taipei 🇹🇼. 先週台北で開かれたアジア・パシフィック魚類会議のサテライト研究会が沖縄美ら海水族館で本日開催されます。当研究室が進めてきた、深海適応の分子メカニズムを含むサメ・エイ類のゲノム進化学研究についてその場で紹介します。 ご興味おありでしたら、 #Squalomix で検索ください。
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 14/05/2025
#ERGAReads | Can #genomic analysis estimate past population size? ⌛️📉 Sequentially Markovian coalescent #SMC methods can lead to misleading estimates. Cross-disciplinary collaboration is needed to interpret them accurately. 🧬 🔗 Read more: www.cell.com/trends/genet... @qmul.ac.uk
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 12/06/2025
#ERGAReads | This week, we highlight Squalomix, our newest associated partner 🦈🧬 #Squalomix tackles key challenges in #elasmobranch genomics through advanced cytological techniques and high-fidelity long-read sequencing. 🔗 f1000research.com/articles/11-... @kurakulabmsm.bsky.social #sharks #rays
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 13/06/2025
New preprint from #Squalomix www.biorxiv.org/content/10.1... Towards bona fide 'whole-genome' analysis encompassing rDNA, tRNA, histones, centromere, elusive HoxC , ... , while featuring genome size change like shown here for the V2R clusters. @ebpgenome.bsky.social‬ @ergabiodiv.bsky.social‬
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Irish Basking Shark Group @irishbaskingshark.bsky.social · 23/05/2025
We have extended our abstract submission to June 1st! Get conference details here: www.baskingshark.ie/conference2025 and submit your abstract here: docs.google.com/forms/d/e/1F...
baskingshark.ie
Conference | The Irish Basking Shark Group
Please join us for the International Conference on Basking Sharks in Galway August 29-31st.
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Shawn Burgess @burgesslab.bsky.social · 08/04/2025
GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline. www.ncbi.nlm.nih.gov/datasets/gen...
ncbi.nlm.nih.gov
Danio rerio genome assembly GRCz12tu
- Danio rerio
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Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 22/05/2025
(3/4) 🌍 The EBP dream-team are sequencing genomes 🧬 to accelerate #research, improve protections, and identify the species that make up critical ecosystems. 🧬Dive into these genomes with @kurakulabmsm.bsky.social, @ergabiodiv.bsky.social, @vertebrategenomes.bsky.social, and many more 🌏
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 03/12/2024
We are based at National Institute of Genetics in Mishima, Japan, close to Suruga Bay >2500m deep & Mt. Fuji >3700m high. #Squalomix #MedakaBase
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/05/2025
Empowering medaka fish biology with versatile genomic resources in MedakaBase www.biorxiv.org/content/10.1101/202…
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RepeatMasker Project @repeatmasker.bsky.social · 05/05/2025
RepeatMasker 4.1.9 released. This release includes fixes for ProcessRepeats (speed issues, and divide-by-zero), a fix for clade-level pHMM (nhmmer) searches, and some minor utility/documentation updates. See the www.repeatmasker.org for more release details.
repeatmasker.org
RepeatMasker Home Page
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Trends in Genetics @cp-trendsgenetics.bsky.social · 05/05/2025
“Intragenomic mutational heterogeneity: structural and functional insights from gene evolution” by Yuichiro Hara & Shigehiro Kuraku (@kurakulabmsm.bsky.social) FREE access till June 24th at this link: authors.elsevier.com/a/1l2K3cQbJF...
Figure 1. Genomic and epigenetic features contributing to and resulting from the intragenomic heterogeneity of mutations.
The genomic regions shown in red and cyan indicate the genomic compartments with the intragenomic heterogeneity.
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 24/04/2025
www.treethinkers.info/post/%E6%96%...
treethinkers.info
新年度近況いろいろ
3月は中旬に札幌での日本生態学会、そして下旬に相模原の北里大での日本水産学会に参加しました。前者には毎回参加しているわけではありませんが、今回は日本の希少生物のゲノム情報の集積状況について紹介しました(発表スライド; さらに参考、以前の記事)。後者の会では発表はありませんでしたが、最新の話題を追うとともに進行中の共同研究やこれから着手する連携研究についての相談も兼ねて参加しました。4月に入り、学振...
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 15/04/2025
Our research on sharks and rays conducted in National Institute of Genetics, Japan, at the foot of Mt Fuji has just been introduced at #PacBioPRISM. #Squalomix Lab HP www.nig.ac.jp/nig/research...
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Zebrafish Rock! @zebrafishrock.bsky.social · 14/04/2025
Learn about the internationally-diverse Phng Lab @riken-bdr.bsky.social 🇲🇾 🇦🇺 🇯🇵 🇨🇳 🇺🇦 🇲🇲 🇮🇳 🐟 #zebrafish @phnglab.bsky.social
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 13/04/2025
Having a glimpse of the Vietnam's Red List, with the same mind about biodiversity and potentials of genomics as we tackle with the Japanese counterpart. vast.gov.vn/web/vietnam-... #PacBioPRISM
vast.gov.vn
Vietnam Academy of Science and Technology
Vietnam Academy of Science and Technology
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 07/04/2025
One week to go! #PacBioPrism #Squalomix
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 30/03/2025
Our research on sharks🦈 & rays will be introduced at #PacBioPrism in Da Nan, Vietnam🇻🇳, on April 15 by Shigehiro Kuraku. #Squalomix
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 06/04/2025
昨日の一般公開、当研究室は、DNA情報に基づいて脊椎動物の進化を辿る研究の意義や手法、とくにサメやエイの貴重な試料の確保について紹介しました。たくさんの方々に来場いただき、さまざまな刺激をいただきました。 www.sut-tv.com/news/single/... #遺伝研一般公開 #Squalomix
sut-tv.com
200種類300本の桜を一般公開 品種の保存を目的に全国から集める 美しさで多くの人を魅了 | テレビ静岡
フジテレビ系列のテレビ局<テレビ静岡>。番組情報、ニュース、イベント、スポーツなど静岡のことならテレしずへ!
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 30/03/2025
Our research on sharks🦈 & rays will be introduced at #PacBioPrism in Da Nan, Vietnam🇻🇳, on April 15 by Shigehiro Kuraku. #Squalomix
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 30/03/2025
Presenting our activity in June at Joint Conf. of Asian Society of Ichthyologists (ASI) Annual Meeting & Indo-Pacific Fish Conf. (IPFC) in Taipei 🇹🇼 Title 'Unraveling shark and ray evolution through genomic exploration' by Shigehiro Kuraku @sighex #IPFC12 #IPFC2025 #ASI2025
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RepeatMasker Project @repeatmasker.bsky.social · 13/03/2025
RepeatMasker 4.1.8 released. A major update to ProcessRepeats has significantly reduced RepeatMasker's memory requirements. Additionally, RepeatMasker now supports the new FamDB 2.0.0 format introduced in Dfam 3.9. See the www.repeatmasker.org for more release details.
repeatmasker.org
RepeatMasker Home Page
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 26/03/2025
www.treethinkers.info/post/%E9%81%...
treethinkers.info
遺伝子推定をオーダー
自分たちでやる必要がなくなったということではありません。自分が、あるいは、他の研究者がNCBIへ登録しリリースされたゲノムアセンブリに付随した遺伝子アノテーションがついていない場合、NCBIへリクエストすることができます。ただし、多様性の高い(動物の場合、血球以外の組織が望まれる)トランスクリプトームデータ(RNA-seqリード in SRA)がすでにNCBIに登録されている場合に限られます。また...
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 26/03/2025
www.treethinkers.info/post/4-5%E3%...
treethinkers.info
4/5に一般公開
当研究室が三島でスタートし、はや四年。研究所の一般公開イベントが今年は4月5日(土)に催されます。私の研究室も、スペースを頂いての展示を初めて行います。研究所のシンボルである桜の時期ということで、研究機関としては珍しい春の開催です。とはいえ、遺伝研としては恒例のイベントです。桜の見ごろの時期と大きくずれてしまわないか、やはり気になります。動物の生体展示はありませんが、動物進化、特にDNA情報に基づいて多様な暮らし方に迫る研究の仕方と成果を紹介します。工樂自身も展示コーナーであれこれ説明する予定です。気が向いたら、ぜひお越しください。イベントは毎年ありますが、私の研究室の展示は毎年はありません。昨年は、当研究室の展示はなかったにもかかわらず、サメの展示がみれると、しかも、生きたジンベエザメがみれると、大きな誤解した方が来観者の中にいたそう、なぜでしょうか!!??だいぶあとになって小耳に挟んだ話です。
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 24/02/2025
Eggcase of the zebra shark (aka leopard shark), Stegostoma tigrinum.
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 30/11/2024
Figures from our review paper - Genomic reconsideration of fish non-monophyly: why cannot we simply call them all ‘fish’? link.springer.com/article/10.1...
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 25/12/2024
youtu.be/_xXfpIc7l2E?...
youtu.be
Squalomix Trailer - Summer 2021
YouTube video by Molecular Natural History Lab at NIG 自然派ゲノム研究室
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Amy Rae Hill @amyraehill.bsky.social · 23/02/2025
Be a shark in a sea of stars! ✨ #pottery
Hand painted teapot and mug featuring luminous, translucent sharks swimming through the dark blue cosmos, embellished by twinkling stars. They have long fins like thresher sharks. Hand painted teapot and mug featuring luminous, translucent sharks swimming through the dark blue cosmos, embellished by twinkling stars. They have long fins like thresher sharks. Top view of small shark on lid.Hand painted teapot and mug featuring luminous, translucent sharks swimming through the dark blue cosmos, embellished by twinkling stars. They have long fins like thresher sharks. Detail of shark at top of mug.Hand painted teapot and mug featuring luminous, translucent sharks swimming through the dark blue cosmos, embellished by twinkling stars. They have long fins like thresher sharks. Detail of shark at bottom of mug.
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Tree-thinkers Lab✨分子生命史研究室 @kurakulabmsm.bsky.social · 24/02/2025
Eggcase of the zebra shark (aka leopard shark), Stegostoma tigrinum.
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