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Yuki Yamashita

@ydymst.bsky.social
101 followers 401 following 41 posts

2nd year PhD student @Hiroshima Univ. I'm interested in the morphology, development, and evolution of bryophytes.

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Yuki Yamashita @ydymst.bsky.social · 06/07/2026
I visited Oxford for Molecular Moss Workshop last week. I was exposed to a lot of nice research and people at the workshop! Oxford is a wonderful place as well. Thank you for every organizers and participants! À bientôt 👋
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Reposted by Yuki Yamashita
Hugues Renault @huguesrenault.bsky.social · 10/03/2026
#JobAlert #PhD 🌱 We are offering a PhD project to explore how transcription factors have shaped the evolution of plant protective barriers. We will support suitable candidates in applying to the @unistra.fr Graduate School competition. Interested? Please get in touch for more information!
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Yuki Yamashita @ydymst.bsky.social · 05/03/2026
Thanks for your comments! As you said, dehydration of spores must be not enough because I immediately put them into a freezer. They may be broken from inside because of water freezing in a spore. Again, I appreciate your advice.
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Yuki Yamashita @ydymst.bsky.social · 04/03/2026
Another possibility comes up. I put spores into a refrigerator just after putting them into a tube with silica gel. Perhaps they may break from inside because of freezing…
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Yuki Yamashita @ydymst.bsky.social · 02/03/2026
I may find the cause of spore sterility... That may be high humidity of culture plate of Marchantia...
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Yuki Yamashita @ydymst.bsky.social · 02/03/2026
My colleague tells me that spores of M. polymorpha cultivated on agar medium are worse (not germinated etc...) than those on soil...... If so, my resource will be useless...
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Yuki Yamashita @ydymst.bsky.social · 02/03/2026
It seems to be fine that spore is stored at 4˚C, -30˚C or even -80˚C.
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Yuki Yamashita @ydymst.bsky.social · 02/03/2026
Perhaps, -30˚C was too harsh and 4˚C is appropriate...?
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Yuki Yamashita @ydymst.bsky.social · 02/03/2026
How should I keep spores of Marchantia polymorpha subsp. ruderalis? Although I have kept them at -30˚C for 1-2 months, they don't germinate so far.
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Adrienne Roeder Lab @roederlab.bsky.social · 23/02/2026
How moss makes a spiral of leaves through a rotating asymmetric division of the apical cell meristem--our paper is out @currentbiology.bsky.social today! @soestrauss.bsky.social Richard Smith, Joe Cammarata www.cell.com/current-biol...
cell.com
Spiral phyllotaxis in the moss Physcomitrium patens emerges from simple division rules of the apical cell
Cammarata et al. explore how cell division orientation generates phyllotaxis in moss with a unicellular meristem. They show that successive rotational divisions in the apical cell are precisely placed...
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Reposted by Yuki Yamashita
Nina Rønsted @ninaronsted.bsky.social · 11/02/2026
We are hiring Tenure-track Assistant Professor and Curator in Bryology at Natural History Museum Denmark, Copenhagen. Duties are collection-based research, curation of >350.000 bryophytes, university teaching and public engagement. Deadline 23 March 2026. Start Jan 2027. lnkd.in/eEaXnNnb
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Reposted by Yuki Yamashita
IBMP | Institut de biologie moléculaire des plantes @ibmp-cnrs.bsky.social · 18/02/2026
🎉 Congratulations to Katarina Kuusk on her successful PhD defense at IBMP (Feb 3, 2026)! Her work bridges structural bioinformatics & plant molecular biology to unravel dynamic P450 metabolons in soybean. 🌱
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Yuki Yamashita @ydymst.bsky.social · 01/01/2026
Happy new year! I wish this year will become one of the best year for you! Me? I just do what I have to do.
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Yuki Yamashita @ydymst.bsky.social · 16/10/2025
I listened to a seminar related to this work. Membrane topology inversion is very interesting. doi.org/10.1126/scie...
doi.org
Membrane topology inversion of GGCX mediates cytoplasmic carboxylation for antiviral defense
Mitochondrial antiviral signaling protein (MAVS) is an adaptor involved in antiviral immunity, but its regulation is not fully understood. We identified carboxylation of MAVS by vitamin K (VK)–depende...
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Yuki Yamashita @ydymst.bsky.social · 09/10/2025
Bryophytes hold a larger gene family space than vascular plants | Dong et al. (2025) Nature Plants rdcu.be/eKcyO This is definitely interesting and important to bryophyte research. I feel this way, but I haven't finished reading it yet. I have no idea when I will finish reading this paper. 😅
rdcu.be
Bryophytes hold a larger gene family space than vascular plants
Nature Genetics - A super-pangenome analysis incorporating 123 newly sequenced bryophyte genomes reveals that bryophytes exhibit a larger number of unique and lineage-specific gene families than...
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Yuki Yamashita @ydymst.bsky.social · 22/09/2025
Wow! Bookmark has been introduced! Amazing!
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Yuki Yamashita @ydymst.bsky.social · 05/09/2025
How wonderful bryophytes are!
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Yuki Yamashita @ydymst.bsky.social · 22/08/2025
Chromosome level assembly and annotation of Cuscuta campestris Yunck. (“field dodder”), a model parasitic plant | Cerda-Herrera (2025) G3 doi.org/10.1093/g3jo...
doi.org
Chromosome level assembly and annotation of Cuscuta campestris Yunck. (“field dodder”), a model parasitic plant
Abstract. We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning
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Reposted by Yuki Yamashita
International Parasitic Plant Society - IPPS @parasiticplants.bsky.social · 21/08/2025
Announcement of a chromosome-level assembly and annotation of #parasiticplant Cuscuta campestris
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Yuki Yamashita @ydymst.bsky.social · 21/08/2025
Plant organ modulates morphological constraints of insect-induced galls: evidence from citizen science data | Bessho-Uehara et al. (2025) Scientific Reports doi.org/10.1038/s415...
doi.org
Plant organ modulates morphological constraints of insect-induced galls: evidence from citizen science data - Scientific Reports
Scientific Reports - Plant organ modulates morphological constraints of insect-induced galls: evidence from citizen science data
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Yuki Yamashita @ydymst.bsky.social · 21/08/2025
To gall researchers, the two papers of my previous supervisor have been out! I am very happy to somewhat contribute one of them. Please check it out! Parasitic-Plant Parasite Rewires Flowering Pathways to Induce Stem-Derived Galls | Udandarao et al. (2025) Plant Direct doi.org/10.1002/pld3...
doi.org
Parasitic‐Plant Parasite Rewires Flowering Pathways to Induce Stem‐Derived Galls
Gall-inducing insects manipulate host plant development, redirecting cellular fate and physiological processes to form novel structures. This phenomenon is even more intriguing when the host itself i...
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Reposted by Yuki Yamashita
Nick Desnoyer @nickdesnoyer.bsky.social · 11/08/2025
To promote the collection, I’ve launched a designer clothing line where synthetic biology meets aesthetics. I will give out 100 free limited edition shirts to the first who retweet and order with their handle in the name! Available here → nickdesnoyer.com 🧵(6/7)
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Yuki Yamashita @ydymst.bsky.social · 10/08/2025
I went to Mt. Norikura at northern Japanese alps last weekend for TA works. The environment was very unique and many plants I’ve never seen were there. Going back to the base, I saw the dynamic changes of the vegetation from alpine zone to subalpine zone. It was a good experience for me.
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Yuki Yamashita @ydymst.bsky.social · 01/07/2025
Parts of gemma development and the timing to determine the dorsoventrality are especially interesting. Besides, I learned the importance of examining all three planes; frontal, sagittal, and transverse, to see a whole picture of gene expression pattern in 3D structure.
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Yuki Yamashita @ydymst.bsky.social · 01/07/2025
Three-dimensional anatomy and dorsoventral asymmetry of the mature Marchantia polymorpha meristem develops from a symmetrical gemma meristem | Spencer et al. (2024) Development doi.org/10.1242/dev....
doi.org
Three-dimensional anatomy and dorsoventral asymmetry of the mature Marchantia polymorpha meristem develops from a symmetrical gemma meristem
Summary: The anatomy, symmetry and gene expression of the Marchantia polymorpha meristem changes during its lifespan, providing a foundational framework for identifying previously unreported mechanism...
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Yuki Yamashita @ydymst.bsky.social · 22/06/2025
Naming is caring. Nat. Plants 11, 1091–1092 (2025). doi.org/10.1038/s414...
doi.org
Naming is caring - Nature Plants
We can now carry in our pockets applications that accurately identify the plants around us. These are interesting tools for researchers, but they also help everyone to appreciate the diversity of the ...
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Yuki Yamashita @ydymst.bsky.social · 22/06/2025
Very interesting work based on careful and precise observation. I like this and really learn a lot from this.
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Yuki Yamashita @ydymst.bsky.social · 22/06/2025
Reproducibly oriented cell divisions pattern the prothallus to set up dorsoventrality and de novo meristem formation in Marchantia polymorpha | Wallner and Dolan (2023) Current Biology www.cell.com/current-biol...
cell.com
Reproducibly oriented cell divisions pattern the prothallus to set up dorsoventrality and de novo meristem formation in Marchantia polymorpha
Wallner and Dolan describe the cell division patterns that form the flat Marchantia prothallus from a single-celled spore. A meristem with an apical stem cell develops on the prothallus to initiate in...
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Yuki Yamashita @ydymst.bsky.social · 11/06/2025
車軸藻クレブソルミディウムのゲノムから見た植物の陸上化 | 堀, 太田 (2016) BSJ Review bsj.or.jp/jpn/general/...
bsj.or.jp
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Yuki Yamashita @ydymst.bsky.social · 11/06/2025
植物の上陸作戦=シャジクモの辿った道 | 坂下 BSJ Review (2010) bsj.or.jp/jpn/general/...
bsj.or.jp
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Yuki Yamashita @ydymst.bsky.social · 06/06/2025
In-insect synthesis of oxygen-doped molecular nanocarbons | Science www.science.org/doi/10.1126/... This research is super interesting! An insect is like a function. Insect(an organic compound) = a new organic compound
science.org
In-insect synthesis of oxygen-doped molecular nanocarbons
Many functional molecules and materials have been produced with organic chemistry or with in vitro enzymatic approaches. Individual organisms, such as insects, have the potential to serve as natural r...
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Yuki Yamashita @ydymst.bsky.social · 06/05/2025
This review is educational to see the field of plant cell biology, especially cell division, the growth and the fate. doi.org/10.1093/plce...
doi.org
Cycling in a crowd: Coordination of plant cell division, growth, and cell fate
Plant cell cycle and division are linked to specific cell fates and respond to growth-related cues, such as metabolic state, cell size, cell shape, and mec
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Yuki Yamashita @ydymst.bsky.social · 06/05/2025
nph.onlinelibrary.wiley.com
Phyllotaxis: is the golden angle optimal for light capture?
See also the Commentary on this article by Sicard, 225: 13–15.
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Yuki Yamashita @ydymst.bsky.social · 10/04/2025
I found Anthoceros agrestis at my university! Tiny horns!
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Yuki Yamashita @ydymst.bsky.social · 07/04/2025
This reading helps us to think about how we manage and drive our research. www.nature.com/articles/s41...
nature.com
Openness guides discovery - Nature Biotechnology
Nature Biotechnology - Openness guides discovery
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Yuki Yamashita @ydymst.bsky.social · 02/04/2025
Merci beaucoup! Je ferai de mon mieux💪
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Yuki Yamashita @ydymst.bsky.social · 01/04/2025
Finally, I start my PhD research at Hiroshima University supervised by Dr. Shimamura! Bon voyage 🚀🚀🚀
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Yuki Yamashita @ydymst.bsky.social · 10/03/2025
Quick action!
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Reposted by Yuki Yamashita
Alexis Licht @alexislicht.bsky.social · 07/03/2025
Dear US colleagues, In response to the Trump administration, my university @univ-amu.fr is setting up a new program dedicated to welcoming American scientists wishing to pursue their work in France. There are several M$ in the budget. www.univ-amu.fr/en/public/ac...
univ-amu.fr
Safe Place For Science: Aix Marseille Université ready to welcome American scientists | Aix Marseille Université
In a context where some scientists in the United States may feel threatened or hindered in their research, our university is announcing the launch of the Safe Place For Science program, dedicated to w...
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Reposted by Yuki Yamashita
Hugues Renault @huguesrenault.bsky.social · 06/01/2025
Dear French and Japanese colleagues, mark your calendars! We are organising the bilateral France-Japan "Frontiers in Plant Biology" symposium. Date: November 19-21, 2025 Location: Strasbourg More information soon! #plantscience
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Yuki Yamashita @ydymst.bsky.social · 01/01/2025
Bonne année!
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Yuki Yamashita @ydymst.bsky.social · 12/12/2024
Ma amie est au Japon! Bienvenue dans mon pays! 🇯🇵
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Yuki Yamashita @ydymst.bsky.social · 21/11/2024
The era of bryophytes is coming!
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Yuki Yamashita @ydymst.bsky.social · 21/11/2024
Meiosis in flowering plants and other green organisms | Harrison et al. (2010) J. Exp. Bot. doi.org/10.1093/jxb/...
doi.org
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Yuki Yamashita @ydymst.bsky.social · 19/11/2024
Given the recent advances in omics technologies and bioinformatics software, if I have enough money, I can do almost anything we want to do. Therefore I have to think hard and deeply about what is interesting, what is important, and what is what I want to dedicate my life to.
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Yuki Yamashita @ydymst.bsky.social · 28/09/2024
Ideally, is it possible to assign quantitative volumes to all factors controlling the development in whatever plants you are researching on? I want to use MorphoGraphX to reconstruct its complete development process in silico.
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Yuki Yamashita @ydymst.bsky.social · 04/05/2024
doi.org/10.1038/s414... 理想的に言えば、発生に関わる全ての要素に定量的数値を与えることができる?(=分子Aは時期BにlongitudinalにC、mediolateralにD、細胞を変化させる的な)MorphGraphX、面白い。
doi.org
Two orthogonal differentiation gradients locally coordinate fruit morphogenesis - Nature Communications
The coordination of cellular behaviors is essential for proper organogenesis. Here the authors show that fruit development in Arabidopsis is governed by time-shifted differentiation gradients that act...
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Yuki Yamashita @ydymst.bsky.social · 27/02/2024
kamounlab.medium.com/move-out-of-...
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Yuki Yamashita @ydymst.bsky.social · 12/02/2024
Hello, Bluesky!
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