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This award was established in June 2022 to encourage graduate students who have achieved outstanding research results and other notable achievements each academic year.

This year, four graduate students received this award.

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However, in a recent study published in PNAS, researchers from The University of Osaka have revealed that circadian clock oscillation in cyanobacteria is controlled by factors intrinsic to one of the proteins that controls it, in a manner that is unaffected by environmental conditions.

Even the smallest, photosynthetic organisms have internal clocks, including cyanobacteria. These microorganisms are vital for aquatic environments, agriculture, and biotechnology. Given their vitality, it is even more important to ensure the correct timing of biological processes for photosynthesis during the day, and respiration at night.

Cyanobacteria are known to possess the simplest known circadian clock, involving only three primary proteins: KaiA, B, and C. It was these proteins that were the focus of the investigation.

“Though the cyanobacterial circadian clock is very simple, and can be reconstructed with three proteins, we still wanted to understand how these simple elements work together,” says lead author, Kumiko Ito-Miwa. “It is critical to understand how the reliability of the circadian rhythm is maintained under different environmental conditions, as it affects an incredibly wide variety of cellular processes.”

To do this, the researchers examined more than 20 mutations in the KaiC clock protein, with disturbed clock periods ranging from 15 to 60 hours. Through this, they were able to demonstrate that the circadian clock could maintain accurate timekeeping both in vitro and in vivo, regardless of environmental changes, through properties inherent to the clock proteins. This included the activity of ATPase, an enzyme responsible for producing chemical energy, which allows cells to perform their duties in various processes.

“The activity of this protein, which acts as the pacemaker of the cyanobacterial clock, did not change in response to different environmental conditions. This property, which appears to be innate to the protein itself, is likely critical for preserving circadian timing despite environmental changes,” explains Kumiko Ito-Miwa, lead author, building on a concept originally proposed and long pursued by Takao Kondo.

The findings suggest that the environment inside cyanobacterial cells may fine-tune the circadian clock to align it with Earth’s 24-hour cycle, offering significant insight into the fundamental question of how living organisms measure time.

Rhythms of KaiC period mutants in cells and in vitro (representative examples).
Even when temperature or light intensity changes, the circadian period of the wild type (normal strain), as well as those of short- and long-period mutants, remains largely unchanged. Moreover, compared with the in vitro clock, the intracellular clock shifts slightly toward the Earth’s 24-hour cycle: short-period mutants lengthen slightly, whereas long-period mutants shorten slightly.

The article, “Intrinsic period stability of the cyanobacterial circadian oscillator
across in vitro and in vivo conditions,” was published in PNAS at DOI: https://doi.org/10.1073/pnas.2526714123

Related links

• Life and Planetary Evolution Science (LIPES) Group

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

Light-regulated enzymatic degradation and spatial patterning through localized irradiation

The article, “Light-Programmable Polyester Networks with Movable Cross-Links for On-Demand Enzymatic Degradation,” will be published in ACS Nano at DOI: https://doi.org/10.1021/acsnano.5c19646

Related links

• Professor Takashima Yoshinori (Researcher Directory)

• Polymeric Materials Design Laboratory

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

In a study recently published in Nucleic Acids Research, researchers from The University of Osaka discovered that the loss of heterochromatin can kickstart genetic changes, potentially resulting in the development of diseases like cancer.

The model showed that RNA-loops (R-loops) accumulate at clusters of repetitive DNA called pericentromeric repeats in response to a process called transcriptional pausing–backtracking–restart (PBR). These accumulated R-loops are then changed into Annealing-induced DNA-RNA-loops (ADR-loops), leading to gross chromosomal rearrangements (GCRs) at constricted parts of a chromosome.

“Previously, we showed that loss of Clr4, the H3K9me2/3 methyltransferase, or its regulatory protein Rik1, increased transcription and abnormal chromosome formation in fission yeast,” explains lead author, Ran Xu. “However, the molecular link between transcription dynamics and GCRs remains poorly defined.”

Heterochromatin forms at pericentromeric repeats. Previous research showed that heterochromatin could prevent GCRs at centromeres by blocking pericentromeric transcription. However, the present study expanded on past findings by providing insights into the mechanism by which GCRs are generated, including through pericentromeric transcription.

The researchers demonstrated that loss of Clr4 can spark an increase in R-loop levels at pericentromeric repeats. After overexpressing the enzyme RNase H1 in cells lacking the clr4 gene, the research team observed reductions in both R-loops and GCRs.

Further experiments highlighted the importance of Tfs1/TFIIS and Ubp3, which are necessary to restart transcription, in R-loop accumulation and GCRs. In cells lacking Clr4, a type of protein called Rad52 built up at pericentromeric repeats. This promoted the development of GCRs, and cells carrying a mutated version of this protein had fewer GCRs because single-strand annealing (SSA), a DNA repair process, was inhibited.

“These data suggest that, when heterochromatin is lost, transcriptional PBR cycles accumulate R-loops at pericentromeric repeats, and Rad52-dependent single-stand annealing converts R-loops into ADR-loops followed by Polδ-dependent break-induced replication (BIR), encouraging GCRs related to disease,” concluded Xu.

This study could have key insights for treating genetic diseases caused by GCRs, like cancer. Although further research is needed to translate these findings into human applications, drugs targeting Rad52 or other genes and proteins involved in GCR accumulation might emerge as key disease treatments.

DNA-RNA Immunoprecipitation (DRIP)-Seq data showing accumulation of R-loops in the heterochromatin-deficient clr4∆ mutant.

The article, “Transcriptional PBR cycles at pericentromeric repeats cause gross chromosomal rearrangements through Rad52-dependent ADR-loop formation,” was published in Nucleic Acids Research at DOI: https://doi.org/10.1093/nar/gkaf1455

Related links

• Professor Takuro Nakagawa (Researcher Directory)

• Laboratory of Molecular Genetics

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

Conference: 2025 NSYSU × UOsaka Science Joint Symposium
Date: Saturday, December 6, 2025, 9:00 AM – 5:00 PM
Organizers: College of Science, National Sun Yat-sen University; Graduate School of Science, The University of Osaka
Venue: International Conference Hall, College of Science, National Sun Yat-sen University

On December 2, we paid a courtesy visit to National Taiwan Normal University and met with three professors: Prof. Wen-Chung Kao, Dean of the College of Interdisciplinary Industry-Academia Innovation, Prof. Cheng-Hung Lin, and Prof. Hui-Ling Sung. We exchanged views on future educational and research collaboration as well as the possibility of holding an AI Workshop using semiconductors and discussed specific approaches for organizing the workshop. We plan to continue discussions toward organizing the workshop.

Furthermore, on December 3, we visited Realtek Semiconductor and Eink, where we received detailed explanations about each company’s business overview and research and development, and viewed their product and technology displays. These visits provided valuable insights for us to design and develop the “Global Researcher Development Intensive Program in Taiwan,” scheduled for the next fiscal year, particularly for shaping the program including company visits.

The following five members from The University of Osaka’s Graduate School of Science visited National Taiwan Normal University:

KONDO Tadashi, Dean, Professor
KUBO Takashi, Associate Dean, Professor
KOSHINO Mikito, Professor
FUJII Ryoko, Assistant Head of Administration
YOKOI Nozomi, Administrative Staff

This visit gave us a great chance to build closer ties with National Taiwan Normal University.

See the back number.

More than 20 years after the discovery of slow earthquakes, which cause weak or no perceptible vibration but associate with slow slip for about a year at maximum, the unified explanation for the characteristics of slow earthquakes does not exist. Up to now, most experimental studies that reproduced slow earthquakes have focused only on the slowness of fault slip. However, what makes slow earthquakes most distinct from regular earthquakes are rather their statistical features revealed through seismic observations. These statistical characteristics of slow earthquakes, however, had rarely been reproduced or explained in laboratory experiments.

“Slow earthquakes have traditionally attracted attention mainly for their slow slip rate, but the statistical properties of their duration and recurrence relative to earthquake magnitude have so far been addressed only in a few limited experiments,” says a study author Yuto Sasaki. “Needless to say, experiments using actual rocks and natural fault grains are of great importance; however, we realized a necessity of simpler physical equivalent, which enables us to directly observe internal structures during deformation. This is a major advantage of our experimental system, as such direct internal observation is usually very difficult in rock-deformation experiments.”

The researchers have prepared very simple “gel jelly beads raft”. As the fault region of slow earthquakes is expected rich in fluid and soft grains, they conceived its physical analog of soft gel jelly beads in a liquid solution. “This table-top experimental system is available even in your home, but it shows a surprising variety of behaviors and offers us a wealth of fascinating clues about slow earthquakes underground,” says Sasaki. “If you put rigid glass beads into a dry cup and mix it slowly, you can feel intermittent and fast scratches. Actually, these scratch events show the statistics similar to regular earthquakes.” However, the mixture of gel jelly beads and a liquid solution shows significantly different features with longer and smaller events, as with slow earthquakes. “You can feel sluggish, intermittent slide by mixing bubble tea, but the two phenomena seem to be fundamentally different.”

In contrast to dry rigid beads, soft wet beads are inefficient in transmitting force and deformation. This property potentially induces longer and isolated small slips. “In retrospect, this experimental system seems to have been well suited for studying fault systems of slow earthquakes, while our prior target was deeper part of tectonic plate,” says Sasaki. “We expect the similar experimental report from high temperature and pressure experiments using rock and fault material.”

Slow earthquakes often occur adjacent to the source regions of regular, destructive earthquakes. “Based on the results, observed slow earthquake statistics could be interpreted as fault conditions,” says Sasaki. This would contribute to probabilistic assessments of earthquakes. Moreover, the longstanding mystery of the mechanisms underlying slow earthquake occurrence is expected to be further addressed not only through laboratory experiments but also through observational studies and geological analyses. “This experimental result will serve as a starting point for further contributions from a wider range of fields, ultimately advancing our understanding of slow earthquakes and enabling better assessment of their influence on conventional, destructive earthquakes,” says Sasaki.

Since the experimental setup used in this study is simple, the observed results can also represent general characteristics of the mixture of soft beads and liquid. “By analyzing the detailed relationship between microscopic bead rearrangements and macroscopic slips, fundamental aspects of sheared soft-matter systems can be revealed, as well as the origin of characteristic features of slow earthquakes. Nothing excites me more than realizing that tabletop experiments in soft matter can unlock the mysteries of both fundamental soft-matter physics and geological-scale phenomena,” says an author Hiroaki Katsuragi.

Cross section of a subduction zone and the source regions of slow earthquakes

The article, “Origin of slow earthquake statistics in low-friction soft granular shear,” was published in Nature Communications at DOI:
https://www.doi.org/10.1038/s41467-025-65230-z

Related links

• Yuto Sasaki (first & corresponding author)

• Soft Matter Earth & Planetary Science Group

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

Here comes an opportunity for students to have hands-on research experiences in a research group of the Graduate School of Science. Students interested in natural sciences or related fields are welcomed to apply our International Summer Program!

For more details, please visit the ISP website below.
https://www.sci.osaka-u.ac.jp/en/international-summer-program-isp/

■ Program Period
July 16 – August 27, 2026

■ Application Period
December 8, 2025 – January13, 2026

■ Contact
If you have any inquiries, please feel free to contact us by email.
Email address: ri-summerprogram@sci.osaka-u.ac.jp