Kanazawa University NanoLSI Podcast – Détails, épisodes et analyse

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Kanazawa University NanoLSI Podcast

Adarsh Sandhu

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Fréquence : 1 épisode/26j. Total Éps: 53

The Kanazawa University NanoLSI Podcast offers updates of the latest news and research at the WPI-NanoLSI Kanazawa University. The Nano Life Science Institute (NanoLSI) at Kanazawa University was established in 2017 as part of the World Premier International (WPI) Research Center Initiative of the Ministry of Education, Culture, Sports, Science and Technology (MEXT). Researchers at the NanoLSI are combining their cutting-edge expertise in scanning probe microscopy to establish ‘nano-endoscopic techniques’ to directly image, analyze, and manipulate biomolecules for insights into mechanisms governing life phenomena such as diseases. Further information WPI-NanoLSI Kanazawa University websitehttps://nanolsi.kanazawa-u.ac.jp/en/

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https://nanolsi.kanazawa-u.ac.jp/en/
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https://nanolsi.kanazawa-u.ac.jp/en/announcements/nanolsipodcast/
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https://nanolsi.kanazawa-u.ac.jp/en/research/researchers/
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https://doi.org/10.1126/sciadv.abq0160
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High speed atomic force microscopy studies provide insights into influenza A viral replication

jeudi 21 novembre 2024 • Durée 04:21

D. Carlero et al, ACS Nano 2024, 18, 30, 19518–19527

Researchers from Kanazawa University's NanoLSI, IMDEA Nanoscience, and CNB-CSIC studied influenza A replication using high-speed atomic force microscopy. They observed that recombinant ribonucleoprotein complexes (rRNPs) can undergo multiple transcription cycles, with RNA structure stability influencing synthesis rates. Their findings offer new insights into viral replication mechanisms and RNA synthesis regulation, opening doors for further research on gene expression control.

NanoLSI Podcast website

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Atomic force microscopy in 3D

jeudi 24 octobre 2024 • Durée 04:46

M.S. Alam et al, Small Methods 2024, 2400287

Atomic force microscopy (AFM) was initially developed to visualize surfaces at nanoscale resolution. Researchers at WPI NanoLSI, Kanazawa University, have now extended AFM for 3D imaging, particularly for flexible nanostructures like carbon nanotubes. They demonstrated that dynamic mode AFM, which uses a vibrating tip, causes less friction and damage than static mode, making it ideal for imaging delicate biological systems like cells, organelles, and vesicles.

NanoLSI Podcast website

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Sensing a biomarker

jeudi 26 septembre 2024 • Durée 05:41

Madhu Biyani and colleagues at NanoLSI, Kanazawa University, have developed a sensitive and selective electrochemical biosensor for detecting the cancer biomarker ADAR1, using new aptamers. This cost-effective tool enables rapid ADAR1 detection in diluted samples, promising improved cancer prognosis and monitoring.

NanoLSI Podcast website

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Exploring hydrogen peroxide eustress effects on cancer cells using microscopy

jeudi 22 août 2024 • Durée 04:28

Yanjun Zhang, Yuri Korchev, and colleagues used hopping probe scanning ion conductance microscopy to study hydrogen peroxide eustress on colorectal cancer cells, revealing varying cell stiffness and gradients. Their findings could lead to new cancer and inflammatory disease therapies.

NanoLSI Podcast website

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Biochemical tails tell a story

jeudi 25 juillet 2024 • Durée 04:46

Mikihiro Shibata and collaborators used high-speed atomic force microscopy to study nucleosome dynamics. They found that nucleosomes without histone tails, particularly H2B and H3, showed increased sliding and DNA unwrapping. These findings highlight the importance of histone tails in chromatin stability and structure.

NanoLSI Podcast website

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Kanazawa University NanoLSI Podcast: Discovering the molecular recognition of technological solids by mutant self-assembling peptides

vendredi 28 juin 2024 • Durée 08:52

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Japan, collaborating with Professor Sarikaya, Seattle, USA.

The research described in this podcast was published in Small in February 2024

Kanazawa University NanoLSI website

https://nanolsi.kanazawa-u.ac.jp/en/

NanoLSI Podcast website

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Kanazawa University NanoLSI Podcast: Researchers observe the structural heterogeneity of a lipid scramblase

vendredi 24 mai 2024 • Durée 06:27

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Holger Flechsig and Clemens Franz from WPI-NanoLSI, at Kanazawa University, in collaboration with Vincent Torre from the International School of Advanced Studies in Italy and former WPI-NanoLSI members Leonardo Puppulin and Arin Marchesi.

The research described in this podcast was published in Nature Communications in January 2024

Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/

Researchers observe the structural heterogeneity of a lipid scramblase

Researchers from Nano Life Science Institute (WPI-NanoLSI), at Kanazawa University report in Nature Communications that TMEM16F, a transmembrane protein that facilitates the passive movement of phospholipids and ions across membranes, explores a larger conformational landscape than previously thought to perform its unique functions. The finding refines our molecular understanding of crucial physiological processes such as blood coagulation and COVID-19 pathogenesis, and highlights the importance of probing membrane proteins in native-like environments.

Lipid scramblases are proteins embedded in cell membranes that play a crucial role in shuffling phospholipids between the two lipid layers that form such cellular boundaries. TMEM16F, a member of the TMEM16 protein family, acts as both a calcium-activated ion channel and a lipid scramblase, meaning that it can facilitate the transfer of both, lipids and ions across the chemical environment outside and inside of the cell. These movements regulate several biological functions such as blood clotting, bone development, and viral entry and are therefore of great physiological and clinical interest. At the molecular level, the TMEM16F architecture has a double-barrelled shape in which two identical polypeptide chains (called subunits), each formed by ten transmembrane (TM) helices, stick together (a process known as dimerization) to form two separate and presumably independent ion and lipid pathways.

Previously, it was thought that TMEM16F might work like a simple gate, with calcium ions serving as keys to unlock the two permeation pathways. Opening and closing the gate to different extents would let lipids and ions cross the plasma membrane alternately. However, structural investigations using cryo-electron microscopy (cryo-EM) -an in vitro technique that can reveal the 3D architecture of purified and frozen proteins at near-atomic resolution – have mostly captured TMEM16F snapshots in inactive conformations, with the ion and lipid gates presumably trapped in a closed state, raising questions about the validity of existing models.

Kanazawa University NanoLSI Podcast: A novel role for S100A11 in focal adhesion regulation

vendredi 10 mai 2024 • Durée 07:15

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Tareg Omer Mohammed, You-Rong Lin, and Clemens M. Franz at the Nano Life Science Institute (WPI-NanoLSI), at Kanazawa University.

The research described in this podcast was published in the Journal of Cell Science in January 2024.

Kanazawa University NanoLSI website
https://nanolsi.kanazawa-u.ac.jp/en/

A novel role for S100A11 in focal adhesion regulation

Researchers at Kanazawa University report in the Journal of Cell Science on a novel role of the small Ca2+ion-binding protein S100A11 [S one hundred A eleven] in focal adhesion disassembly.

S100A11 is a small Ca2+ion-activatable protein with an established role in different cellular processes involving actin cytoskeleton remodeling, such as cell migration, membrane protrusion formation, and plasma membrane repair. It also displays F-actin binding activity and localizes to actin stress fibers, but its precise role in regulating these structures remained unclear.

In their study, Tareg Omer Mohammed, You-Rong Lin, and Clemens M. Franz together with colleagues from the Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, in Japan, and Karlsruhe Institute of Technology, in Germany, report a novel localization of S100A11 to disassembling focal adhesions at the end of contractile stress fibers in HeLa and U2OS cells. Specifically, S100A11 transiently appears at the onset of focal adhesion disassembly, reliably marking the targeted adhesion sites for subsequent disassembly. Interestingly, S100A11 leaves focal adhesion sites before the completion of disassembly, indicating that S100A11 plays a specific role in the initiation of adhesion site disassembly, rather than the disassembly process itself.

So what are focal adhesions anyway and what can we learn from them?

Focal adhesions are integrin-containing cell/matrix adhesion sites enabling cells to adhere to the cellular environment and to apply cellular contraction forces during extracellular matrix remodeling. Directed cell migration requires the coordinated assembly of new adhesion sites at the front, and disassembly at the rear of the cell, and better understanding mechanisms regulating focal adhesion turnover is, therefore, an important goal in cell migration and invasion research. The newly discovered role of S100A11 in focal adhesion disassembly extends insights into the molecular mechanisms underlying focal adhesion site disassembly.

Kanazawa University NanoLSI Podcast: Researchers observe what ubiquitination hinges on

Saison 4

vendredi 26 avril 2024 • Durée 06:28

Researchers observe what ubiquitination hinges on

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by Hiroki Konno and Holger Flechsig at Nano Life Science Institute (WPI-NanoLSI), Kanazawa University.

The research described in this podcast was published in Nano Letters in December 2023

Kanazawa University NanoLSI website

https://nanolsi.kanazawa-u.ac.jp/en/

Researchers observe what ubiquitination hinges on

Researchers at Nano Life Science Institute (WPI-NanoLSI), Kanazawa University report in Nano Letters how the flexibility of a protein hinge plays a crucial role in the transfer of proteins in key cell processes.

Ubiquitination – the addition of the protein ubiquitin – is a key stage in many cell processes, such as protein degradation, DNA repairs, and signal transduction. Using high-speed atomic force microscopy (AFM) and molecular modelling, researchers led by Hiroki Konno and Holger Flechsig at WPI-NanoLSI, Kanazawa University have identified how the mobility of a ubiquitination related enzyme hinge allows ubiquitination to take place.

So what was known already about ubiquitination?

Previous studies have identified a number of enzymes that facilitate ubiquitination, including an enzyme that activates ubiquitin (E1), an enzyme that conjugates it (E2), and an enzyme that catalyzes ubiquitin protein joining (that is, a ligase, E3) to a target protein. The HECT-type E3 ligase is characterized by a HECT domain that comprises an N lobe with the E2-binding site and a C lobe with a catalytic Cys residue, A flexible hinge connects the two lobes, leading to the hypothesis that ubiquitination is facilitated by the rearrangement of the protein around this hinge. Konno and their collaborators deployed their high-speed atomic force microscope to hunt for evidence that this was the case.

Kanazawa University NanoLSI Podcast: Chromatin Accessibility: A new avenue for gene editing

Saison 4

vendredi 12 avril 2024 • Durée 04:53

Chromatin Accessibility: A new avenue for gene editing

Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, led by Yusuke Miyanari.

The research described in this podcast was published in Nature Genetics in February 2024

Kanazawa University NanoLSI website

https://nanolsi.kanazawa-u.ac.jp/en/

Chromatin Accessibility: A new avenue for gene editing

In a study recently published in Nature Genetics, researchers from Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University explore chromatin accessibility, that is, endogenous access pathways to the genomic DNA, and its use as a tool for gene editing.

Our DNA is protected from unwanted external modifications by forming structures called nucleosomes that consist of threads of DNA wound around chunks of special proteins known as histones. This unique coiled shape prevents the access of undesirable molecules to a cell’s DNA. However, for vital genetic functions—such as DNA repair—the right set of proteins require access to these DNA fragments. This phenomenon known as ‘chromatin accessibility’ involves a privileged set of protein molecules, many of which are still unknown.

Now, researchers from Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University, led by Yusuke Miyanari, have used advanced genetic screening methods to unravel chromatin accessibility and its pathways.

So how did they go about it?

For the investigation the team used a combination of two technologies—CRISPR screening and ATAC-see. While the former is a method to suppress the function of a desired set of genes, the latter is a means to identify which ones are essential for chromatin accessibility. Thus, using this method all genes playing a crucial role in chromatin accessibility could be pinned down.

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Kanazawa University NanoLSI Podcast – Détails, épisodes et analyse

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