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Ranking 1 Access:1107

2015.08.06

Lecture
Part 2: Helicobacter pylori and Gastric Cancer

Species name: Helicobacter pylori
Stanford University Stanley Falkow

Helicobacter pylori lives in the human stomach. It causes gastritis, ulcer disease and even gastric cancer. Some H. pylori can inject a protein, CagA, into gastric epithelial cells. CagA interacts with the tight junctions that bind cells together and with signaling molecules affecting motility and proliferation. CagA is associated with ulcer disease and cancer but we don't understand how it works to favor malignancy. Not long ago in history most humans carried H. pylori ; the incidence of carriage and gastric cancer is dropping but there is evidence that this microbe also had a protective effect on human health.

Ranking 2 Access:696

2013.07.03

Eukaryotic cell
Locomotion of Amoeba proteus

Species name: Amoeba proteus
University of Hyogo, Graduate School of Life Science Yukinori Nishigami

Amoeba proteus exhibit active cell locomotion. During locomotion, cytoplasm actively flows toword direction of locomotion.

Ranking 3 Access:498

2017.08.29

Eukaryotic cell
Macrobiotus sp.

Species name: Macrobiotus sp.
Tokyo Metropolitan Government Bureau Swerage,

The size of Macrobiotus is about 0.2 – 1.0 mm. The body is covered with a thin chitin film, with spiny bristles, armor plates. There are four pairs of footsteps, with nails at the tip. Macrobiotus have fourth pair of legs with nails at the tip. They usually live in soil. The form that I'm slow in action and walk slowly is similar to a bear, so it's called a bear bug. The tooth needle taken out of the mouth is stuck into food, and it's crowded, and a pharynx, to work, more, I suck at contents. Slowly walking figure resembles a bear so it is called water bears.

微生物図鑑

Ranking 4 Access:375

2014.07.19

Model (CG)
Movement of Actin-associated Myosin-II (Cross-Bridge) during Muscle Contraction

Species name: Rabbit
Osaka City Univ Eisaku KATAYAMA

The first part of the movie indicates the movement of individual myosin-head (crossbridge), based on conventional "Tilting-Leverarm Hypothesis". Such movement was proposed from the characteristic features of the atomic models of myosin-S1 in the absence and the presence of ATP, together with the well-known experimental evidence that "the motor-domain does not appreciably rotate during the Power-Stroke". Hence, this hypothesis claims that the Power-Stroke is essentially the transition between strongly actin-bound rigor-structure (1DFK: lever-arm is extended) and ATP-bound kinked structure (1DFL). If the motor-domain is immobilized on actin, the lever-arm moiety should swing along the actin filament, The latter half of the movie exhibits the revised crossbridge-cycle we have proposed according to our direct observation of in vitro sliding actomyosin by Quick-Freeze Deep-Etch Replica Electron Microscopy (Ref. 1, 2). We noticed that the actual images of actin-sliding myosin cannot be explained by the conventional hypothesis as above, suggesting the presence of a new conformer whose crystal structure is not yet reported. After extensive search, we finally found that SH1-SH2 crosslinked myosin could be a good candidate of the new conformer whose lever-arm bends to the opposite side of ATP-bound kinked structure (Ref.3-5). Since we could successfully reconstruct its low-resolution 3-D model by a new version of single-particle-analysis (Ref. 5). Taking the results of time-resolved chemical crosslinking into consideration, we revised the scheme of crossbridge-cycle including the new conformer (Ref.5). .The conformational change shown in the movie is compatible with all the images we actually observed under in vitro actin-sliding conditions. [References] 1. Katayama E. The effects of various nucleotides on the structure of actin-attached myosin subfragment-1 studied by quick-freeze deep-etch electron microscopy. J Biochem. 1989 Nov;106(5):751-70. 2: Katayama E. Quick-freeze deep-etch electron microscopy of the actin-heavy meromyosin complex during the in vitro motility assay. J Mol Biol. 1998 May 1;278(2):349-67. 3: Katayama E, Ohmori G, Baba N. Three-dimensional image analysis of myosin head in function as captured by quick-freeze deep-etch replica electron microscopy. Adv Exp Med Biol. 1998;453:37-45. 4: Katayama E, Ichise N, Yaeguchi N, Yoshizawa T, Maruta S, Baba N. Three-dimensional structural analysis of individual myosin heads under various functional states. Adv Exp Med Biol. 2003;538:295-304. 5: Kimori Y, Baba N, Katayama E. Novel configuration of a myosin II transient intermediate analogue revealed by quick-freeze deep-etch replica electron microscopy. Biochem J. 2013 Feb 15;450(1):23-35. 6. Andreev OA, Reshetnyak YK. Mechanism of formation of actomyosin interface. J Mol Biol. 2007 Jan 19;365(3):551-4.

Ranking 5 Access:344

2019.10.28

Others
Evidence of swimming P-Chlamydomonas cell lens effect (Kenichi Wakabayashi, Laboratory for Chemistry and life science, Tokyo Institute of Technology)

The Biophysical Society of Japan annual meeting executive committee 2019

Green algae Chlamydomonas recognizes the direction of the light source by the eye point and exhibits phototaxis. The eye point performs highly directional photoreception by lining the photoreceptor on the cell membrane with a dye layer acting as a light reflector. We isolated a mutant that swims in the opposite direction to the wild type strain, and found that the cause was a defect in the pigment layer. The reason for swimming in the opposite direction was that the eye point that lost the pigment layer felt that the light collected by the lens effect through the cell was stronger than the light coming from the front and misidentified the direction of the light source. However reviewers said Chlamydomonas can never be a convex lens. We put the letter P (the acronym for photo) in the optical path of the microscope, and thought that it could be countered if the letter P was visible on the cell. The results are as you can see (Ueki, Ide et al., 2016 PNAS) Microscope: Olympus BX-53, Camera: Omron Sentec STC-MCA5MUSB3

Ranking 6 Access:325

2014.03.13

Eukaryotic cell
Euglenoid movement of Euglena

Species name: Euglena
Department of Biology, Faculty of Science, Kobe University Masashi HAYAKAWA

Euglenoid movement of Euglena

Ranking 7 Access:308

2017.08.02

Eukaryotic cell
SPOC(Myofibril in auxotonic condition)

Waseda Univerisity Shin'ichi ISHIWATA

SPOC(Myofibril in auxotonic condition)

Ranking 8 Access:300

2015.10.30

Model (CG)
Updated centipede model for Mycoplasma mobile gliding

Species name: Mycoplasma mobile
Osaka City Univ Makoto MIYATA, Tasuku HAMAGUCHI

supplemented to a scientific paper Prospects for the gliding mechanism of Mycoplasma mobile Makoto Miyata, Tasuku Hamaguchi (Osaka City University) doi:10.1016/j.mib.2015.08.010 end user license: CC BY-NC-ND 4.0

Miyata M, Hamaguchi T, Prospects for the gliding mechanism of Mycoplasma mobile. Current Opinion in Microbiology. 29, 15-21.

Ranking 9 Access:300

2019.10.17

Meeting
Dr. Nagai wearing a Hyottoko mask at the party of annual meeting of the Biophysical Society 2019

The Biophysical Society of Japan annual meeting executive committee 2019

Dr. Nagai wearing a Hyottoko mask at the party of annual meeting of the Biophysical Society 2019

Ranking 10 Access:298

2019.10.17

Meeting
Dr. Nagai at the party of annual meeting of the Biophysical Society 2019

The Biophysical Society of Japan annual meeting executive committee 2019

Dr. Nagai at the party of annual meeting of the Biophysical Society 2019

Ranking 11 Access:297

2019.10.28

Others
Retina 2: Swim inside the retina (Shinya Sato, Graduate school of biostudies, Kyoto Unibersity)

The Biophysical Society of Japan annual meeting executive committee 2019

Summary: Retinas were isolated from mice expressing fluorescent proteins in the cytoplasm of whole cells, and tomographic images were taken at 1 µm intervals from the surface to 200 µm deep using a multiphoton microscope. The moving image is obtained by reconstructing the stack image data in the depth direction into a continuous tomographic image from the side of the retina by image processing, and it feels like swimming in the retina. <Highlights> The photoreceptor nuclei are beautifully arranged vertically in 9 to 10 layers for a reason. It is said that nocturnal organisms such as mice have a special structure of photoreceptor nucleus in which heterochromatin is localized in the central part, and this acts as a microlens, thereby guiding incident light linearly. Camera:Olympus multiphoton laser scanning microscope

Ranking 12 Access:291

2020.01.23

Lecture

Osaka City University Makoto Miyata

The research team of Dr. Makoto Miyata (Graduate School of Science, Osaka City University), conducted the research of "Harmonized supramolecular motility machinery and its diversity " supported by the Ministry of Education, Culture, Sports, Science and Technology by 47 research teams from 2012 to 2018. Based on the experimental results and discussions obtained from this study, they proposed for the first time the origin and evolution of all motility discovered so far. This content was published in "Genes to Cells", a European journal of the Molecular Biology Society of Japan, on January 20, 2020.

Ranking 13 Access:282

2019.10.17

Meeting
Fireworks at the annual meeting of the Biophysical Society 2019

The Biophysical Society of Japan annual meeting executive committee 2019

Fireworks were launched at a social gathering held at the 57th Annual Meeting of the Biophysical Society of Japan

Ranking 14 Access:279

2019.12.05

Lecture
Prof. Nobuhiro Go's Talk on

Species name: Talk
Tokyo Institute of Technology Akio Kitao on behalf of Prof. Nobuhiro Go

This talk was given in Symposium "Present and Future of Theoretical Biophysics", Februray 14, 2019 at Kyoto University upon Prof. Go's 80th birthday. This reseach achievement was published in a journal, Biophysics and Physicobiology.

Ranking 15 Access:278

2015.06.25

Model (CG)
Flagellar helical form: Normal, CW rotation. Polymorphic transition.

Faculty of Life and Environmental Scienses, Prefectural University of Hiroshima Shin-ichi Aizawa

Bacterial flagellar filament has polymorphic transition ability, which can switch between a set of helical forms (straight, Normal coiled and curly) in response to flagellar motor rotation, pH, salinity, and temperature changes.

Ranking 16 Access:278

2019.10.28

Others
Chlamydomonas graphy (Kenichi Wakabayashi, Laboratory for Chemistry and life science, Tokyo Institute of Technology)

The Biophysical Society of Japan annual meeting executive committee 2019

The culture solution of green algae Chlamydomonas was placed in a square dish, and a membrane-permeable reactive oxygen species reagent that induces positive phototaxis was added. This was placed on the light box, and an OHP sheet with white letters “BIOPHYSICS” was written under the dish. After standing for about 3 minutes, the cells gathered clearly at the character. After about 4 minutes from pulling out the sheet, it diffuses and the characters become invisible. This video is the reverse playback of the last 4 minutes at 20x speed. It is possible to draw using Chlamydomonas' accurate light source recognition and rapid light mobility. Camera: SONY Cyber-shot DSC-RX100M2

Ranking 17 Access:277

2019.10.17

Meeting
Dr. Kabayama at the party of annual meeting of the Biophysical Society 2019

The Biophysical Society of Japan annual meeting executive committee 2019

Dr. Kabayama at the party of annual meeting of the Biophysical Society 2019

Ranking 18 Access:277

2019.10.28

Others
Distribution of Lgr5-positive stem cells in mouse small intestinal organoids (Masanori Tomita, Central Research Institute of Electric Power Industry)

The Biophysical Society of Japan annual meeting executive committee 2019

Organogoids were constructed by culturing Lgr5-positive stem cells isolated from mouse small intestine crypts, and Z-stack images were obtained using a multiphoton excitation microscope. The purpose was to take a 3D construction image, but when the Z stack image was converted into a movie, it became a beautiful movie like a fireworks display that colored the summer night. Since the multiphoton excitation microscope was used, the internal structure of the organoid can be seen, but it looks like fireworks reflected in the clouds. Green fluorescence is GFP (Lgr5-positive stem cells), red fluorescence is Lgr5-positive stem cells expressing tdTomato by tamoxifen treatment and some of the differentiated cells derived from it, and blue fluorescence is Hoechst33258 (cell nucleus). Nikon, A1R MP

Ranking 19 Access:269

2016.11.14

Prokaryotic cell
Motility of Paenibacillus sp. NAIST15-1 (3)

Species name: Paenibacillus sp.
Graduate School of Biological Sciences, Nara Institute of Science & Technology Kazuo Kobayashi

Time-lapse analysis of colony formation. One microliter of Paenibacillus sp. suspension was spotted onto a 1.5% agar plate, which was then incubated at 37°C. The process of colony formation was analyzed by time-lapse light microscopy. Time-lapse images were collected every 1 min for 16 h after inoculation. Playback speed, ×1,440. Scale bar, 2 mm.

Genetic Analysis of Collective Motility of Paenibacillus sp. NAIST15-1

Ranking 20 Access:267

2019.10.28

Others
A trillionth of a globe (Yuuka Nimura, Graduate school of science, Osaka University)

The Biophysical Society of Japan annual meeting executive committee 2019

Multi-component GUV composed of phospholipid POPC and SM, glycolipid GM3, Cholesterol, and fluorescently labeled peptide was photographed in 3D. Red represents Texas Red-DHPE, and green represents NBD-labeled synthetic transmembrane peptide. Usually GUV moves during observation and it is difficult to shoot in 3D, but 3D imaging became possible by reducing the laser output thoroughly using a GaAsP detector and suppressing vibrating due to laser irradiation. The appearance of the Ld phase island floating in a GUV with a diameter of about 20 µm is like a small Earth. A1R + (Nikon) Lens: Apo, 60x, NA1.40, Oil

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