Biology Biophysics

Researchers at Nano Life Science Institute (WPI-NanoLSI), Kanazawa University report in Nature Communications a high-speed atomic force microscopy study of the structural dynamics of sodium ion channels in cell membranes. The findings provide insights into the mechanism behind the generation of cell-membrane action potentials.

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.

Researchers at Kanazawa University report in Frontiers in Molecular Biosciences a computational method to predict the placement of proteins on AFM substrates based on electrostatic interactions.

Researchers at Kanazawa University report in Cell Reports how alterations in the nuclear pores lead to the degradation of anti-tumor proteins.

Researchers at Kanazawa University report in STAR Protocols procedural details and tips for nanoendoscopy-AFM, for capturing images of nanoscale structures inside living cells.

Researchers at Kanazawa University report in Nature Communications how calcium ions can block sodium ion channels located in cell membranes. Structural analysis and computer simulations made it possible to identify where and why calcium ions get stuck.

Researchers at Kanazawa University report in Science Advances high-speed atomic force microscopy experiments that show the structural and chemical changes in an enzyme thought to play a vital role in modulating the strength of neural connections.

Researchers at Kanazawa University report in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) high-speed atomic force microscopy experiments that show how ligands associated with stimulating and suppressing activation of the TRPV1 protein increase and decrease the molecule’s structural variations. The observations provide insights into how these heat- and chilli-sensing proteins function.

A group including Osaka Metropolitan University researchers discovered that the rhodopsin—a protein in the eye that detects light—of whale sharks has changed to efficiently detect blue light, which penetrates deep-sea water easily. The amino acid substitutions–one of which is counterintuitively associated with congenital stationary night blindness in humans—aid in detecting the low levels of light in the deep-sea. Although these changes make the whale shark rhodopsin less thermally stable the deep-sea temperature, allows their rhodopsin to keep working. This suggests that the unique adaptation evolved to function in the low-light low-temperature environment where whale sharks live.

Researchers at Kanazawa University report in ACS Nano how high-speed atomic force microscopy can be used to study the biomolecular mechanisms underlying gene editing.

Osaka Metropolitan University researchers have used 100 seconds of laser irradiation to generate convection currents that selectively accelerate biochemical reactions—due to the photothermal effect—by concentrating biofunctional molecules at the cell surface. Using this method, useful molecules can be transported into cells at concentrations a hundred to a thousand times lower than with conventional methods. Furthermore, they also succeeded in selectively introducing small molecules into intracellular organelles usually impossible at low concentrations (hundreds of pmol/L) as well as inducing cell death in targeted cells by concentrating anticancer active peptides into them at concentrations so low that they would not be conventionally effective (several tens of nmol/L).

Researchers at Kanazawa University report in Nano Letters the discovery of a biomolecular dynamical process likely relevant to gene expression. The process, revealed by means of high-speed atomic force microscopy, involves DNA and its packaging molecules.

Researchers at Kanazawa University report in Nano Letters how high-speed atomic force microscopy can be used to assess the effectivity of spike-neutralizing antibodies for preventing COVID-19. The use of such antibodies offers a promising alternative to vaccines.

Osaka Metropolitan University scientists discovered the principle of light-induced acceleration of antigen–antibody reaction, allowing for simple, ultrafast, and highly sensitive detection of proteins. The researchers introduced target proteins and probe particles with modified antibodies selectively binding to the target proteins into a small channel and applied irradiation with infrared laser light. They achieved, for the first time, the rapid measurement of trace amounts of attogram-level target proteins after only 3 minutes of laser irradiation. These findings will potentially contribute to breakthroughs in the development of systems for ultra-early diagnosis of various diseases.

Using cryogenic electron microscopy, a research team from the Research Center for Artificial Photosynthesis (ReCAP) at Osaka Metropolitan University has revealed, for the first time, the structures and binding environments of pigments bound to a protein called a photosynthetic antenna of the marine green macroalga Codium fragile. The team’s results extend our knowledge about the molecular mechanism by which blue-green light—the only light available in deep seawater—is efficiently utilized for photosynthesis.

- Discovery of potential treatment target networks for gene dysregulation uniquely found in patients with autism spectrum disorder - Published in ‘Molecular Psychiatry,’ an international journal of molecular psychiatry

Osaka Metropolitan University researchers introduced seven proteins, thought to let bacteria swim by switching the direction that their helical bodies spiral, into a strain of synthetic bacterium with minimal genetic information. As a result, they confirmed that the synthetic bacterium named syn3, which is normally spherical, formed a helix that could swim by spiraling. Further investigation revealed that only two of these newly added proteins were required to make syn3 capable of minimal swimming. This swimming synthetic bacterium can be said to be the smallest mobile lifeform genetically, as it contains the fewest number of genes.

In a study recently published in the Journal of Extracellular Vesicles, researchers from Kanazawa University use high-speed microscopy to capture the dynamics of nanosized sacs released from cells.

6th NanoLSI Symposium: International symposium on Nanoprobe Technology for Understanding Molecular Systems in Kanazawa, Japan

Researchers from Osaka University have found that serum albumin interferes with β2m amyloid fibril formation through macromolecular crowding. Monitoring serum albumin concentrations could therefore help prevent patients from developing dialysis-related amyloidosis, a serious complication of long-term dialysis.

Researchers at The University of Tokyo create a geometric representation of thermodynamic systems and apply it to self-replicating processes, which may help improve our understanding of the physical constraints of living organisms

Researchers at Kanazawa University report in Communications Biology that using common chemicals for fixing living cell samples for microscopy studies causes membrane proteins to aggregate.

Researchers at Kanazawa University report in ACS Nano the development of a nanoparticle that acts as a heater and a thermometer. Inserting the nanoparticle in living cells results in a heat spot that, by switching it on and off, enables the controlled modulation of local cellular activities.

Researchers at Kanazawa University report in The Journal of Physical Chemistry Letters how to simulate 3D atomic force microscopy images of out-of-equilibrium systems involving biomolecules. The approach makes use of a celebrated equation from thermodynamics applicable to non-equilibrium situations.

Researchers at Kanazawa University report in Biophysics and Physicobiology how to optimize high-speed atomic force microscopy experiments on live cell membranes, so that moving objects like molecules can be properly followed from frame to frame.

A machine rapidly and robustly separates cancer cells from blood samples, overcoming challenges with currently available techniques.

Tile patterns in which the same shape is laid out without gaps are found in the compound eyes of insects. Hexagonal tile patterns are common while shrimp eyes have a square pattern. We investigated tile pattern formation using Drosophila and revealed that the compound eye tile pattern is controlled by a geometrical division mechanism, Voronoi tessellation, in addition to physical constraints determined by the combination of the regular distribution and growth of the individual eyes.

Researchers at Kanazawa University elucidate in Frontiers in Molecular Biosciences how small biocontainers enclosed by membranes are involved in a disease called ATTRv amyloidosis.

Electrical stimulation of nerve fibers could promote the growth of the myelin sheath, a protective layer around neurons that is crucial for transmitting nerve impulses. The finding, published in the journal Biofabrication, introduces a new paradigm in the treatment of diseases where the myelin sheath is progressively lost, leading to muscular atrophy, hand and foot deformities, gait abnormalities, and paralysis.

Giants in History: Gopalasamudram Narayanan Ramachandran (8 October 1922 – 7 April 2001) is best known for developing the Ramachandran plot to understand the structure of short chains of amino acids, known as peptides.