Now, researchers from The University of Osaka have reported a new way to bring ancient proteins back to life. The study, published in ACS Omega, has revealed that the developed methodology can help generate ancestral rhodopsins that can be tested experimentally in bacteria.

A wide range of microbes express proteins called microbial rhodopsins, which are embedded in the cell membrane and play a variety of roles, including pumping ions across the membrane or sensing light. Scientists have long wondered how members of this single family can possess such a wide array of functions, with investigations involving analyzing the protein sequences to determine their evolutionary history.

“Rhodopsins all have seven transmembrane domains that are very similar, but their extramembrane domains, which extend inside and outside of the cell, vary dramatically,” says lead author, Haruto Ishikawa. “This makes it very challenging to use standard sequence alignment techniques to trace the evolution of rhodopsin sequences from their shared ancestral proteins.”

To tackle this problem, the researchers analyzed the sequences of two different microbial rhodopsins, schizorhodopsins and heliorhodopsins, using an approach that specifically accounts for insertions and deletions in the extramembrane domains. Based on this technique, they reconstructed ancestral schizorhodopsin and heliorhodopsin sequences and expressed them in bacteria.

“The results were very exciting,” explains Yasuhisa Mizutani, senior author. “Both the ancestral schizorhodopsin sequence and the ancestral heliorhodopsin sequence produced stable, mature proteins in Escherichia coli that had a distinctive color and showed characteristic spectral properties, just like existing rhodopsins.”

Similar to contemporary schizorhodopsins, the ancestral schizorhodopsin showed light-driven proton-transport activity. In contrast, the ancestral heliorhodopsin did not pump ions, consistent with current heliorhodopsins.

“Our findings show that sequence reconstruction that takes insertions and deletions into account can successfully generate full-length ancestral rhodopsins that can be experimentally produced and tested,” explains Ishikawa.

The researchers have made their analytical pipeline, ConsistASR, available for other investigators to use. The ConsistASR workflow could help reconstruct and engineer other ancestral proteins, providing functional insight into protein evolution.

When E. coli cells producing ancestral rhodopsin (Anc-SzR) were illuminated, the pH of the surrounding solution increased. This result supports that the ancestral rhodopsin absorbs light and, like extant schizorhodopsins, transports hydrogen ions (H⁺) into the cells.

The article, “Resurrecting Full-length Ancestral Schizorhodopsins and Heliorhodopsins with Structure-guided, Indel-aware Sequence Reconstruction,” has been published in ACS Omega at https://doi.org/10.1021/acsomega.6c03010.

Related links

• Associate Professor (Lecturer) ISHIKAWA Haruto (Researcher Directory)

• Mizutzni Laboratory, Laboratory for Biophysical Chemistry

• Eurkalert!
• AlphaGalileo
• Asia Research News
• ResOU（Research at Osaka University）website

They were welcomed by Prof. Tadashi Kondo, Dean of the Graduate School of Science and Atsushi Takahashi, Vice Dean and Chair of the International Exchange Committee, along with members of the International Affairs Committee and related staff. The two sides held discussions aimed at moving toward full-scale implementation of the Double Degree Program (DDP) agreement concluded in June 2024. During the meeting, they shared information on laboratories that already have ongoing exchanges, as well as laboratories in overlapping research fields and areas in which they hope to further expand collaboration.
Taking this visit as an opportunity, both universities confirmed that they will make use of the DDP agreement to proceed with concrete arrangements for student acceptance and dispatch. They also shared various operational issues that need to be addressed in order to implement these exchanges.

Based on these discussions, we will continue to strengthen the cooperative relationship between the two universities and further examine concrete steps toward student and research exchanges, including the DDP.

(Scenes from the DDP signing ceremony:https://www.sci.osaka-u.ac.jp/en/news/9991_1/ )

[Visitors]
Prof. Luisella Celi, Vice Rector for Research
(Department of Agricultural, Forest and Food Sciences）
Prof. David Lembo, Vice Rector for International Relations
(Department of Clinical and Biological Sciences）
Prof. Federico Maria Petrucci, Rector’s Delegate for Humanities and Social Sciences Strategic Research
(Department of Philosophy and Education Sciences）
Prof. Stefania Maria Beolé, Rector’s Delegate for Natural and Life Sciences Strategic Research
(Department of Physics）
Mr. Stefano Palmieri, Press Office
Ms. Mariasilvia Ciola, Rector’s Advisor for International Projects
Dr. Ugo Falciola, Head of Commercial Office, the Consulate General of Italy in Osaka

[The University of Osaka]
Prof. Tadashi Kondo, Dean, the Graduate School of Science
(Department of Earth and Space Science)
Prof. Atsushi Takahashi , Vice Dean and Chair of the International Exchange Committee
(Department of Mathematics)
Prof. Hajime Nanjo, Member of the International Exchange Committee
(Department of Physics)
Prof. Nobuto Yoshinari , Member of the International Exchange Committee
(Department of Chemistry)
Prof. Yasuhiro Funahashi, Member of the International Exchange Committee
(Department of Chemistry)
Assoc. Prof. Osamu Urakawa , Member of the International Exchange Committee
(Department of Macromolecular Science)
Assoc. Prof. Tomoyuki Furuya, Member of the International Exchange Committee
(Department of Biological Sciences)
Assoc. Prof. Hirokazu Odaka, Member of the International Exchange Committee
(Department of Earth and Space Science)
Dr. Yuri Kamon(Lecturer), Member of the International Exchange Committee
(Center for International Affairs, Office of Research Administration)
Assoc. Prof. Luca Baiotti , International College

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Registration >> https://forms.cloud.microsoft/r/MZJafQufit
Please register in advance so we can prepare! However, walk-ins are also very welcome.

<Contents>
This event is for all you who want to overcome your weaknesses in English while having fun, who are interested in English, and who want to practice communicating in the English you learn, this is a great opportunity for you! You can get together to play games in English with international students and Japanese students and improve your English skills by receiving appropriate feedback from a native English-speaking instructor.
We are looking forward to your participation.

<Date>
Thursdays, June 18, 25, July 2, 9, and 23

<Time>
12:20〜13:05 Lesson offered by English instructor
13:05〜13:20 Free chat (you can leave any time if you take 3rd period class)

<Location>
Science Bldg. B208

<Instructor>
Shawn Andersson

<Contact>
ri-international@sci.osaka-u.ac.jp (Graduate School of Science, A115)

Back number: English Café 2025, English Café 2024

Note: This information is also available on KOAN.

She was welcomed by Prof. Atsushi Takahashi, Vice Dean and Chair of the International Exchange Committee, and Lecturer Yuri Kamon, a member of the International Exchange Committee, from the Graduate School of Science, as well as Prof. Noriko Okubo and Prof. Mari Shimizu from the Graduate School of Law and Politics. During the meeting, the participants discussed future collaboration.

Building on the academic exchange agreements that our Graduate School of Science and the Graduate School of Law and Politics have concluded with the University of Bremen, the participants introduced the distinctive features of their respective faculties/graduate schools and shared information on the current status of international student acceptance. They also exchanged views on further developing educational and research collaboration.

It was also noted that Japanese can be studied at the University of Bremen’s Language Center and that these courses are very popular. In addition, it was shared that our Graduate School of Science is currently hosting two exchange students from the University of Bremen.

Taking this visit as an opportunity, we will further strengthen cooperation between the two universities and promote international research exchange and human resource development.

[Visitor]
Dr. Mandy Boehnke
（Vice President for International Affairs, Academic Qualification, and Diversity, University of Bremen）

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Now, researchers from Japan have found an overlapping two-factor system that plays an important role in controlling when and how these cells differentiate. In a study published this month in Cell Reports, researchers from The University of Osaka have revealed that two proteins with very similar functions are key regulators of early steps in cellular development and maturation.

Embryonic stem cells can develop into all the different types of cells present in the adult body, from brain cells to liver cells, through a process called differentiation. This process is tightly regulated by activating and repressing factors that bind to the promoters of developmental genes to maintain them in a ‘poised’ state, where these genes can either be switched on or kept off as needed.

“A key mechanism for inhibiting the expression of genes associated with stem cell differentiation involves repressor complexes such as CoREST,” says lead author, Takamasa Ito. “However, it remains unclear how CoREST-mediated repression is stably maintained and which other factors help in repressing expression of these genes.”

To explore this, the researchers tested the role of two proteins, RLF and ZFP292, which previous studies had suggested may help regulate stem cell gene expression. They looked at where these factors bound themselves across the genome and deleted these factors, both individually and together, to determine the effect on gene expression.

“The results were very striking,” explains senior author, Chikashi Obuse. “We found that RLF and ZFP292 play virtually the same role, in that they stabilize the CoREST complex at gene promoters in embryonic stem cells to repress gene expression.”

The presence of either RLF or ZFP292, or both together, at these promoters prevented stem cells from drifting toward differentiation. When these proteins were lost, promoters that were normally repressed became active, leading to the expression of genes associated with differentiation.

“Our results show that RLF and ZFP292 modulate the activity of the CoREST complex to carefully control gene expression in stem cells,” says Ito.

These findings may lead to the development of new techniques for maintaining stem cell quality for research and clinical applications. They also help advance our understanding of diseases caused by dysregulated gene expression and could potentially be applied to develop new treatments.

Overview of the study.
Left: In wild-type cells, RLF/ZFP292 support the proper function of the CoREST complex, leading to the removal of active histone marks and preventing excessive expression of differentiation-associated genes.
Right: In the absence of RLF/ZFP292, CoREST complex function is impaired, resulting in an increase in active histone marks and elevated expression of differentiation-associated genes. Consequently, the undifferentiated state cannot be maintained, and cells undergo differentiation.

The article, “RLF/ZFP292 stabilize CoREST-linked LSD1 engagement at bivalent promoters to safeguard pluripotency,” was published this month in Cell Reports at DOI: https://doi.org/10.1016/j.celrep.2026.117293

Related links

• Department of Biological Sciences, Laboratory of Genome Structure and Function

• Eurkalert!
• AlphaGalileo
• Asia Research News
• ResOU（Research at Osaka University）website

A total of 18 participants attended (7 undergraduate students from the School of Science, 9 graduate students from the Graduate School of Science, 1 undergraduate and 1 graduate student from other schools.). The workshop provided an intensive learning opportunity for participants from a wide range of disciplines and academic levels, covering the full process from AI fundamentals to data collection, training, and implementation.

On the first day, participants learned the basics of AIoT and edge AI, including the fundamental concept of on-device inference, and then proceeded with the setup of the AMB82-mini. They worked on introductory tasks such as audio classification and image classification, and also learned about recent trends and demonstrations in the fields of vision and audio.

On the second day, the program focused on the data preparation process required for implementation, including data collection using the device. In the final session, participants implemented their systems on mini cars and took part in a time-trial race. The event concluded with a lively atmosphere, as participants cheered and compared the different behaviors of the cars.

We would like to express its sincere gratitude to the faculty members and student tutors from NTNU for their invaluable cooperation and support in making this workshop possible.

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They were welcomed by Prof. Tadashi Kondo, Dean of the Graduate School of Science; Prof. Takashi Kubo, Vice Dean; Prof. Atsushi Takahashi, Vice Dean and Chair of the International Exchange Committee; and Lecturer Yuri Kamon, a member of the International Exchange Committee. During the meeting, the participants exchanged views on future collaboration and on a joint symposium scheduled to be held at the University of Osaka in October this year.

In the afternoon of the same day, a research presentation session was held, featuring presentations by two NSYSU faculty members and four students interested in the Double Degree Program (DDP). Faculty members from our Graduate School in related fields also attended, and the session provided a meaningful opportunity for academic exchange through lively questions and discussion. In addition, a laboratory tour was organized after the session, helping the visitors deepen their understanding of our research environment.

Building on the discussions during this visit, we will continue preparations for the successful joint symposium and further strengthen the cooperative relationship between the two universities.

【visitors】
Prof. Jyh-Tsung Lee, Dean, the College of Science
Prof. May-Ru Chen, Associate Dean, the College of Science
Associate Prof. Cheng-Chau Chiu, Associate Vice President for Academic Affairs
Assistant Prof. Chung-Hsin Yang, Assistant Professor, the College of Science
Prof. Toshio Kasai, the College of Science

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Period: From Wednesday, August 12 to Friday, August 14, 2026.

Researchers, as part of a major international collaboration, reported evidence hinting at the existence of a never-before-seen but predicted exotic bound state known as an η′-mesic nucleus. These valuable findings will be published this month in Physical Review Letters.

Physicists have theorized that under certain conditions, short-lived particles called mesons – which only exist for less than ten-millionth of a second – can become temporarily trapped inside a nucleus, forming an exotic bound system. Measuring mesic nuclei could help scientists understand how the strong nuclear force, which binds atomic nuclei together, behaves and how the vacuum structure changes in extremely high-density environments.

“One particle of particular interest is the η′ meson,” says senior author Kenta Itahashi. “It is unusually heavy compared with related particles, and physicists expect that its mass changes when it exists inside nuclear matter. Observing this phenomenon would provide valuable information about how particle masses are generated in the universe.”

To search for the η′-mesic nuclei, the international collaboration carried out a high-precision experiment using a powerful particle accelerator in GSI Helmholtzzentrum für Schwerionenforschung, Germany. They utilized a beam of high-energy protons bombarded on a carbon target to produce η′-mesic states. The energetic proton beam excites the carbon nucleus, producing η′ mesons, which form a bound state with the carbon nucleus with a certain probability. The excitation energies of the carbon nuclei were measured by analyzing the energy of deuterons –the simplest atomic nucleus made of one proton and one neutron– produced forward in the reaction using a high-resolution spectrometer, Fragment Separator (FRS). Researchers employed a special detector called WASA, which was originally developed and constructed in Uppsala, Sweden, to selectively measure high-energy protons that get out from the target, looking for signs that an η′ meson had been created and captured inside the nucleus, otherwise known as decay signals. 

“With our new experimental setup combining the FRS and the WASA, we can identify structures in the data that match theoretical signatures of η′-mesic nuclei,” explains lead author Ryohei Sekiya. “Our analysis suggests that these bound states were indeed formed.”

The resultant excitation spectrum of the carbon nucleus measured in the experiment is displayed in Fig, indicating possible formation of the η′-mesic nuclei. The team’s findings indicate that the mass of the η′ meson may decrease inside nuclear matter, supporting theoretical predictions and providing rare experimental insight into how the properties of particles change in super high-density environments.

“Our measurements provide important new clues about how mesons behave in nuclear matter,” says Itahashi. “This brings us closer to answering deep, fundamental questions about how matter acquires mass, as well as how the vacuum structure changes inside atomic nuclei.”

Future experiments are planned to increase the precision of measurements and search for additional decay signals that could confirm the existence of η′-mesic nuclei. As researchers continue their search, each new result furthers our understanding of the fundamental physical laws that govern the universe.

Excitation-energy spectrum of the carbon-11 nucleus obtained in the present experiment. The excitation energy on the horizontal axis is defined such that zero corresponds to the production of an η′ meson at rest in vacuum. Negative values correspond to bound states of the η′ meson and the nucleus. The circles represent the experimental data, and the vertical bars indicate statistical uncertainties. The solid curve shows the theoretical spectrum that best reproduces the experimental data, while the dotted curve represents the estimated contribution from background processes. The two observed peak structures suggest the existence of η′ meson bound states in an inner (blue) and outer (blue) nuclear orbits in the carbon-11 nucleus.

The article, “Excitation Spectra of the ¹²C(p,d) Reaction near the η’-Meson Emission Threshold Measured in Coincidence with High-Momentum Protons,” will be published in Physical Review Letters at https://doi.org/10.1103/6vsl-ng7x
This article has been selected for “Featured in Physics” at https://journals.aps.org/prl/highlights.

Related links

• Department of Physics, Nuclear Experiment Group

• Eurkalert!
• AlphaGalileo
• Asia Research News
• ResOU（Research at Osaka University）website

Please click the link below for more details.
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