Hidekazu HIROAKI, Ph.D.
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h-hiroaki.bsky.social
Hidekazu HIROAKI, Ph.D.
@h-hiroaki.bsky.social
創薬科学研究者。タンパク質科学・NMR構造生物学・アミロイド研究・天然変性タンパク質研究。研究に関する内容をこちらに掲載します。おもに自分の読もうとしている論文の備忘録です。大学院生募集中。5月に大学院入試説明会が開催されます。趣味はチヌグレセイゴのフカセ釣りです。
Reposted by Hidekazu HIROAKI, Ph.D.
Transcription factor EBF1 is essential for B cell differentiation. Zolotarev et al. show that tyrosines in its intrinsically disordered region are required for phase separation, DNA binding, BRG1 recruitment and chromatin remodeling.
Read more here:
➡️ tinyurl.com/gad350828
February 20, 2024 at 8:51 PM
Reposted by Hidekazu HIROAKI, Ph.D.
💪 Small but mighty! This JIPB mini-review explores the remarkable dual-action mechanism of #Arabidopsis cryptochromes. PlantScience onlinelibrary.wiley.com/doi/10.1111/...
February 28, 2024 at 1:20 PM
Reposted by Hidekazu HIROAKI, Ph.D.
Interplay Between Intracellular Transport Dynamics and Liquid‒Liquid Phase Separation
Interplay Between Intracellular Transport Dynamics and Liquid‒Liquid Phase Separation
Live-cell single-particle tracking of quantum dots reveals the complex interplay between nonequilibrium dynamics and liquid–liquid phase separation (LLPS). Intracellular diffusion and active transport are reduced after LLPS, due to increased molecular crowding and heterogeneity of intracellular environments. Additionally, LLPS is regulated by intracellular dynamics: the reduced intracellular diffusion promotes stress granule (SG) assembly, and microtubule-associated transport facilitates SG coalescence. Abstract Liquid‒liquid phase separation (LLPS) is a ubiquitous process in which proteins, RNA, and biomolecules assemble into membrane-less compartments, playing important roles in many biological functions and diseases. The current knowledge on the biophysical and biochemical principles of LLPS is largely from in vitro studies; however, the physiological environment in living cells is complex and not at equilibrium. The characteristics of intracellular dynamics and their roles in physiological LLPS remain to be resolved. Here, by using single-particle tracking of quantum dots and dynamic monitoring of the formation of stress granules (SGs) in single cells, the spatiotemporal dynamics of intracellular transport in cells undergoing LLPS are quantified. It is shown that intracellular diffusion and active transport are both reduced. Furthermore, the formation of SG droplets contributes to increased spatial heterogeneity within the cell. More importantly, the study demonstrated that the LLPS of SGs can be regulated by intracellular dynamics in two stages: the reduced intracellular diffusion promotes SG assembly and the microtubule-associated transport facilitates SG coalescences. The work on intracellular dynamics not only improves the understanding of the mechanism of physiology phase separations occurring in nonequilibrium environments but also reveals an interplay between intracellular dynamics and LLPS.
onlinelibrary.wiley.com
March 7, 2024 at 2:51 PM
Reposted by Hidekazu HIROAKI, Ph.D.
Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies https://www.biorxiv.org/content/10.1101/2024.03.14.584939v1
Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies https://www.biorxiv.org/content/10.1101/2024.03.14.584939v1
miRNA-repressed mRNAs and Ago proteins are known to be localized to RNA-processing bodies, the subce
www.biorxiv.org
March 15, 2024 at 1:18 AM
Reposted by Hidekazu HIROAKI, Ph.D.
Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies https://www.biorxiv.org/content/10.1101/2024.03.14.584939v1
Amyloid Beta Oligomers Accelerate ATP-Dependent Phase Separation of Ago2 to RNA Processing Bodies https://www.biorxiv.org/content/10.1101/2024.03.14.584939v1
miRNA-repressed mRNAs and Ago proteins are known to be localized to RNA-processing bodies, the subce
www.biorxiv.org
March 15, 2024 at 1:18 AM
Reposted by Hidekazu HIROAKI, Ph.D.
Post-Doctoral Fellowship in Molecular Biophysics #ScienceJobs #AcademicSky jobrxiv.org/job/biol...
Post-Doctoral Fellowship in Molecular Biophysics
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
March 14, 2024 at 9:19 PM
2025年度YLC教員募集(情報開示:2024年3月15日(金)9:00、締切り:2024年5月1日(水)12:00)
www.iar.nagoya-u.ac.jp/public/3039/
創薬研究を志して、ぜひ名古屋大学YLCにチャレンジしたいという方はぜひご連絡ください。特にタンパク質凝集やLLPSやIDPを標的とした創薬研究に興味がある方、一緒にやりましょう!
March 15, 2024 at 7:26 AM
Reposted by Hidekazu HIROAKI, Ph.D.
Call for nominations : the 2024 Varian Young Investigator Award at Euromar 2024, deadline April 15, to to recognize a promising scientist within the first 12 years after their PhD, nominations procedure -> posted 03/06/2024 listes.services.cnrs.fr/wws/arc/nmr/... #NMRnews #NMRchat #NMR 🧲
March 7, 2024 at 3:12 PM
#春から名大 のみなさん、合格おめでとうございます。名古屋大学には薬剤師を養成する薬学部はありませんが、大学院からは「創薬科学研究科」があります。名古屋大学内外の様々な学部を卒業した学生さんを、その背景分野を問わず幅広く受け入れています。
www.ps.nagoya-u.ac.jp/graduate_cou...
将来、医薬品や化粧品や健康食品を生み出す研究に関わりたい、人々の健康に分子・細胞の力で役立ちたい、と思う方は、ぜひ、研究科のウェブページをご訪問ください。
それでは4月に東山キャンパスでお会いしましょう、
Enjoy science!
March 8, 2024 at 9:36 AM
物欲番長 年度末予算で購入できないかしら
www.benq.com/ja-jp/ideaca... BenQ手元実演Webカメラ(ノイキャンマイク機能付き)これは講義の配信とかに便利では?あと試料実物を見ながらの共同研究者とのディスカッションや、ウェブを通じた実験手技の共有などにも 
ideaCam S1 Pro ¥31,800
February 27, 2024 at 7:57 AM
セミナーが面白かったら、どこが面白かったか、どこを深堀りすればもっと面白くなるか、ポジティブにその面白さを言語化していきたい。小さな「知的成功体験」を積み上げていくことで、いろいろな次元での研究プロセス(先行研究調査も立派な研究プロセスの一部)での自己肯定感を上げていってほしいのだ。
February 26, 2024 at 1:53 PM
Conformational strains of pathogenic amyloid proteins in neurodegenerative diseases
Dan Li & Cong Liu 
Nature Reviews Neuroscience volume 23, 523–534 (2022)
www.nature.com/articles/s41...
February 26, 2024 at 1:06 PM
Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain
Rakesh Kumar et al.,
Nature Communications 15, 2024, 965
www.nature.com/articles/s41...
BRICHOS流行の兆し・・・
Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain - Nature Communications
This study identifies potential aggregation hotspots on the fibril surface of Alzheimer’s disease associated Aβ42 fibrils, which are blocked by the anti-amyloid chaperone-like domain BRICHOS.
www.nature.com
February 26, 2024 at 1:04 PM
長良川のアユと河口堰 川と人の関係を結びなおす honto.jp/netstore/pd-...
著者蔵治 光一郎 (編)
February 26, 2024 at 1:00 PM
速攻で発注しました、この内容は買うしかないっしょ

Interface 2024年 04月号
honto.jp/netstore/pd-...

数学100[すぐに使える数式&プログラム付き!]

第6章
AIの数学
6-1 線形モデルの定義/6-2 線形回帰モデルの学習方法:最小2乗法/6-3 線形回帰モデルの学習方法:勾配降下法/6-4 過学習に対抗するための線形回帰モデルの変形/6-5 ニューラル・ネットワーク・モデルの定義/6-6 ニューラル・ネットワーク・モデルの学習/6-7 活性化関数/6-8 重みの更新アルゴリズム/6-9 モデル性能を測るための計算式「評価指標」
February 26, 2024 at 12:54 PM
今日の文献セミナーは、2演題ともとても面白かった。
February 26, 2024 at 12:42 PM
今日は研究室の送別会であった。ノンアルコール、ケーキを囲んでの送別会、楽しかったし、イベントを企画してしきったM1諸氏の企画力・結束力にも脱帽した。終了した皆さん、社会人になっても、身に付けたいろいろな知識や観察力思考力を利用して、enjoy scienceを続けてほしいです。修了おめでとう!
February 26, 2024 at 12:39 PM
February 15, 2024 at 5:32 AM
各位 こっそり?参加者募集サイトがオープンしていますよ~ 

第52回内藤コンファレンス 
テーマ:物理的・機械的視点が拓く生物学
会 期:2024年10月1日(火)~2024年10月4日(金)
会 場:シャトレーゼ ガトーキングダム サッポロ(札幌市)
ポスター募集期間:2024年2月6日(火)正午 ~ 3月12日(火)正午
ということでstiffnessの研究とか機械刺激とか、もちろん相分離も
February 15, 2024 at 5:26 AM

[Program C]
This hands-on program of #IUPAB2024 provides a CHARMM-GUI/GENESIS workshop held in Kobe to learn MD simulations.
Yuji Sugita (RIKEN, Japan)
Wonpil Im (Lehigh Univ, USA)
For an application → x.gd/vpVP9
February 14, 2024 at 10:22 AM

#IUPAB2024 [Program F]
This program includes an introduction to the developments and applications of optical tweezers and correlated microscopy in biological research by IQB, The University of Tokyo and LUMICKS.
For an application → x.gd/vpVP9
x.gd
February 14, 2024 at 10:21 AM
Reposted by Hidekazu HIROAKI, Ph.D.
I don't have examples of *my* work (publication is still a WIP) but I can point to some work from my colleagues!

(Picture from https://doi.org/10.1146/annurev-biophys-042910-155245 but if you search the article on Google scholar you'll get a free pdf result)

(Short 🧵 as I take my train ride home)
July 6, 2023 at 10:58 PM
Reposted by Hidekazu HIROAKI, Ph.D.
To assess, we used @HNNsolver’s biophys model of a cortical column under external drive to predict mechanisms of the FC-ERP features after the stop signal (P2, N2, P3). A sequence of drives strikingly similar to those proposed to produce sensory ERPs can accomplish this. (4/)
October 31, 2023 at 2:07 AM