Talin’s springy role in force transmission

Cell biology has possibly never jumped to the next level in the same way.

In multicellular organisms, cell migration and mechanosensing are essential for cellular development and maintenance. These processes rely on talin, the key focal adhesion — or FA — protein, central in connecting adjacent cellular matrices and enabling force transmission between them.

Talins are commonly considered fully extended at FAs between actin filaments — or F-actin — and the anchor-like integrinreceptor.

Yet, a research team led by Kyoto University have previously observed that the actin network constantly moves over FAs as a single unit: a unique phenomenon contradicting prevailing notions.

“This begs the question: how does talin manage to simultaneously maintain the intercellular connection while transmitting force?” asks corresponding author Sawako Yamashiro at KyotoU’s Graduate School of Life Sciences.

Most significantly, the team’s results reveal a new mode of force transmission in which dynamic molecular stretching bridges the extracellular matrix and flowing F-actin moving at different speeds. This discovery underscores the necessity of molecular elasticity and random coupling for sufficiently transmitting force.

“On a human scale, this phenomenon can be visualized as a super flexible anime character. He is gripping onto a train passing at around 50 km/h,” illustrates Yamashiro.

The train represents the flowing F-actin, while a station platform is the substrate. The superhero plays the talin FA protein that would either be carried away unstretched or remain on the substrate.

“Occasionally, however, when both ends of talin are firmly anchored, it gets stretched by the pull because some parts of this protein can unfold like a spring,” explains Yamashiro.

Aided by intracellular fluorescent talin single-molecule imaging, Yamashiro’s team observed and calculated that approximately 4% of the talin links the F-actin and the substrate via an elastic transient clutch. In contrast, the remaining majority are bound to either end.

These findings also call for revising the role of molecular unfolding, updating the traditional view that it functions as a mechanosensor and a shock absorber when molecules unfold under external force.

“However, our results suggest that molecular unfolding facilitates the transmission of force rather than absorbing it,” says coauthor Dimitrios Vavylonis at Lehigh University.

“We can expect further use of intracellular single-molecule microscopy to witness other possible intra- and extra-cellular superheroic behaviours, such as talin’s elastic transient clutch,” concludes coauthor Naoki Watanabe, also at KyotoU’s Graduate School of Life Sciences.

The paper “Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin” appeared on 20 December 2023 in Nature Communications, with doi: 10.1038/s41467–023–44018-z

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Wider bandwidth quantum infrared spectroscopy

Our understanding of the world relies greatly on our knowledge of its constituent materials and their interactions. Recent advances in materials science technologies have ratcheted up our ability to identify chemical substances and expanded possible applications.

One such technology is infrared spectroscopy, used for molecular identification in various fields, such as medicine, environmental monitoring, and industrial production. However, even the best existing tool — the Fourier transform infrared spectrometer or FTIR — utilizes a heating element as its light source. Resulting detector noise in the infrared region limits the devices’ sensitivity, while physical properties hinder miniaturization.

A research team led by Kyoto University has addressed this problem by incorporating a quantum light source. Their innovative ultra-broadband, quantum-entangled source generates a relatively wider range of infrared photons with wavelengths between 2 μm and 5 μm.

“This achievement sets the stage for dramatically downsizing the system and upgrading infrared spectrometer sensitivity,” says Shigeki Takeuchi of the Department of Electronic Science and Engineering.

Another elephant in the room with FTIRs is the burden of transporting mammoth-sized, power-hungry equipment to various locations for testing materials on-site. Takeuchi eyes a future where his team’s compact, high-performance, battery-operated scanners will lead to easy-to-use applications in various fields such as environmental monitoring, medicine, and security.

“We can obtain spectra for various target samples, including hard solids, plastics, and organic solutions. Shimadzu Corporation — our partner that developed the quantum light device — has concurred that the broadband measurement spectra were very convincing for distinguishing substances for a wide range of samples,” adds Takeuchi.

Although quantum entangled light is not new, bandwidth has thus far been limited to a narrow range of 1 μm or less in the infrared region. This new technique, meanwhile, uses the unique properties of quantum mechanics — such as superposition and entanglement — to overcome the limitations of conventional techniques.

The team’s independently developed chirped quasi-phase-matching device generates quantum-entangled light by harnessing chirping — gradually changing an element’s polarization reversal period — to generate quantum photon pairs over a wide bandwidth.

“Improving the sensitivity of quantum infrared spectroscopy and developing quantum imaging in the infrared region are part of our quest to develop real-world quantum technologies,” remarks Takeuchi.

The paper “Ultra-broadband quantum infrared spectroscopy” appeared on 12 January 2024 in Optica, with doi: 10.1364/OPTICA.504450

Lights, detector, action! was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

She could tell you why diamonds are her best friends

Besides being “a girl’s best friend,” diamonds have broad industrial applications, such as in solid-state electronics. New technologies aim to produce high-purity synthetic crystals that become excellent semiconductors when doped with impurities as electron donors or acceptors of other elements.

These extra electrons — or holes — do not participate in atomic bonding but sometimes bind to excitons — quasi-particles consisting of an electron and an electron hole — in semiconductors and other condensed matter. Doping may cause physical changes, but how the exciton complex — a bound state of two positively-charged holes and one negatively-charged electron — manifests in diamonds doped with boron has remained unconfirmed. Two conflicting interpretations exist of the exciton’s structure.

An international team of researchers led by Kyoto University has now determined the magnitude of the spin-orbit interaction in acceptor-bound excitons in a semiconductor.

“We broke through the energy resolution limit of conventional luminescence measurements by directly observing the fine structure of bound excitons in boron-doped blue diamond, using optical absorption,” says team leader Nobuko Naka of KyotoU’s Graduate School of Science.

“We hypothesized that, in an exciton, two positively charged holes are more strongly bound than an electron-and-hole pair,” adds first author Shinya Takahashi. “This acceptor-bound exciton structure yielded two triplets separated by a spin-orbit splitting of 14.3 meV, supporting the hypothesis.”

Luminescence resulting from thermal excitation can be used to observe high-energy states, but this current measurement method broadens spectral lines and blurs ultra-fine splitting.

Instead, Naka’s team cooled the diamond crystal to cryogenic temperatures, obtaining nine peaks on the deep-ultraviolet absorption spectrum, compared to the usual four using luminescence. In addition, the researchers developed an analytical model including the spin-orbit effect to predict the energy positions and absorption intensities.

“In future studies, we are considering the possibility of measuring absorption under external fields, leading to further line splitting and validation due to changes in symmetry,” says Université Paris-Saclay’s Julien Barjon.

“Our results provide useful insights into spin-orbit interactions in systems beyond solid-state materials, such as atomic and nuclear physics. A deeper understanding of materials may improve the performance of diamond devices, such as light-emitting diodes, quantum emitters, and radiation detectors,” notes Naka.

The paper “Spin-Orbit Effects on Exciton Complexes in Diamond” appeared on 26 February 2024 in Physical Review Letters, with doi: 10.1103/PhysRevLett.132.096902

If Marilyn Monroe Were a Scientist was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

New technoogy to infer gene regulatory networks efficiently and accurately

The Human Genome Project generated the first sequence of the human genome, revealing a kind of blueprint of human biology. Two decades later, the field of gene regulatory networks describes a complex system where thousands of genes regulate each other to create appropriate gene expression dynamics.

However, more work is needed to fully understand these networks and determine their precise nature. Current approaches either estimate gene regulation indirectly or utilize accurate and direct but time-consuming, repetitive methods.

A research group led by Kyoto University has now developed a highly accurate method to semi-automatically estimate gene regulatory networks in multicellular organisms. The method involves measuring time-series gene expression and applying the team’s proprietary RENGE computational model.

“RENGE may help identify the key factors for cell differentiation and potentially control the fate of specific cells,” says corresponding author Masato Ishikawa of KyotoU’s Institute for Life and Medical Science.

Researchers can determine regulatory gene expression using the relatively accurate gene knockout method, where if a gene A is eliminated, a gene B — that A had regulated — is exposed.

The latest single-cell CRISPR technology, which can measure expression changes from large-scale individual knockouts, comes with a caveat: the distinction between directly and indirectly regulated genes is unclear. Knocking out one gene inevitably affects the expression of genes downwind in the network.

Ishikawa and his colleagues addressed the issue by measuring the expression levels in a time series and adapting their mathematical model to estimate gene regulatory networks.

“When we verified RENGE’s accuracy, we obtained results that outperformed existing methods in both simulation data and measured expression data of human iPS cells,” adds Ishikawa.

Using RENGE to maximize information obtained from gene knockout, the team could identify a gene regulatory network containing 103 genes expressing human pluripotency, which was highly consistent with findings accumulated over decades of research in molecular biology.

“However, the beauty is that we could obtain the same results from only one RENGE experiment. Furthermore, we found that transcription factors that regulate the same target genes in this regulatory network tend to work as protein complexes, among which one may be a key factor for pluripotency,” elaborates Ishikawa.

The inherent versatility of this method allows for estimating regulatory networks in various other life systems beyond iPS cells.

“RENGE may inspire new technologies such as producing artificially manipulated cells with specific functions,” remarks Ishikawa.

The paper “RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations” appeared on 28 December 2023 in Communications Biology, with doi: 10.1038/s42003–023–05594–4

Gene expression technology set to semi-automation was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

Global methane emissions automatically detected in satellite imagery using AI

As global temperatures rise to record highs, the pressure to curb greenhouse gas emissions has intensified. Methane is particularly targeted because its significant global-warming potential in the short term exceeds carbon dioxide by over 80-fold.

However, monitoring methane emissions and compiling their quantities have been challenging due to limiting trade-offs with existing detection methods.

Now, a research team including Kyoto University and Geolabe, USA has developed a method to automatically detect methane emissions at a global scale.

“Our approach can potentially provide methane detection at high frequency and high resolution from point sources, paving the way for a systematic quantification method,” says lead author Bertrand Rouet-Leduc of KyotoU’s Disaster Prevention Research Institute and Geolabe.

Rouet-Leduc further suggests that their method may help prioritize and automatically validate atmospheric mitigation of methane, which currently accounts for approximately one third of global warming.

Multispectral satellite data has emerged as a viable methane detection tool in recent years, enabling routine measurements of methane plumes at a global scale every few days. However, significant noise plagues these methane data, and until now, detections have been limited to very large emissions and have required human verification.

In contrast, the team has trained an AI to automatically detect methane leaks over 200kg/h, accounting for over 85% of the methane emissions in well-studied, large oil and gas basins.

“With satellite measurements, trade-offs must be made between spatial coverage, spatial and temporal resolution, and spectral resolution and associated detection accuracy. AI partially offsets these trade-offs,” explains co-author Claudia Hulbert, also of Geolabe.

Methane plumes are invisible and odorless, so they are typically detected with specialized equipment such as infrared cameras. The difficulty in finding these leaks from space goes without saying, akin to finding a needle in a haystack. Leaks are distributed around the globe, and most of the methane plumes are relatively small, making them easy to miss in satellite data.

The group’s collaborative work represents a key step towards the precise, systematic monitoring of methane emissions, anywhere on Earth, every few days.

“Automation is paramount when analyzing large areas. We were surprised that AI can automate the process and dramatically outperform the human eye in detecting small methane plumes, “ reflects Rouet-Leduc.

“In our next phase, we plan to integrate additional satellites in a global study of methane emissions.”

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The paper “Automatic Detection of Methane Emissions in Multi-Spectral Satellite Imagery Using a Vision Transformer” is appearing on May 14th, 2024 in Nature Communications, with doi: 10.1038/s41467–024–47754-y

Interview with Nature Communications editor: https://youtu.be/X8NRQ63Hnvw

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Pituitary hormone signaling realigns biological clock for jet lag recovery

Jet lag is all in the mind. What exactly lags has more to do with the brain’s hypothalamus than the jet.

A misalignment of the body’s internal clock following jet travel across multiple time zones causes sleep deprivation and physical discomfort. The master clock in the tiny suprachiasmatic nucleus — or SCN, in the anterior of the hypothalamus — keeps the departure time and requires several days to adjust to the destination time.

While the exact cause of jet lag remains a mystery, a team of researchers from Kyoto University and Kansai University posits that pivotal vasopressin signaling in neuroendocrine circuits of the hypothalamus and anterior pituitary may have a role in the SCN’s pacemaker.

“The role of rhythm generation by this extra-SCN neuroendocrine-anterior pituitary system might have gone unnoticed had it not been for the advent of intercontinental jet travel in the 1950s, which caused an artificial and uniquely human experience,” says research fellow Hitoshi Okamura of KyotoU’s Graduate School of Medicine.

Subsequent studies revealed that SCN lesions abolished all circadian rhythms in the body, and that isolated SCNs can generate robust circadian rhythms. This discovery has led researchers to believe that only neuronal circuits of SCN clockwork can adjust jet lag to new light-dark cycles.

Previous research found that global inhibition of vasopressin receptors V1a and V1b signaling eliminated jet lag. Okamura’s team is now trying to identify the critical sites in those receptor systems. Thus far, the researchers have determined that vasopressin and its receptor V1b in the hypothalamic-anterior pituitary systems can help maintain the original time during jet lag.

To date, there are no effective medications for the syndrome, mainly because current drugs target only the SCN. The revelation of the hypothalamus-pituitary system orchestrating a synchronized response to the body’s shaken circadian rhythm has inspired the development of more effective treatments.

“The development of vasopressin inhibitors on multiple targets — not only V1a in the SCN but also V1b in the pituitary — could significantly help mitigate jet lag,” offers Yoshiaki Yamaguchi of Kansai University’s Faculty of Chemistry, Materials, and Bioengineering.

“Addressing how the different parts of neuroendocrine systems work collectively on the cellular clockwork in SCNs is an important step towards a deeper understanding of how our biological clocks maintain time even during rapid light fluctuations,” reflects Okamura.

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The paper “An intact pituitary vasopressin system is critical for building a robust circadian clock in the suprachiasmatic nucleus” appeared on 16 October 2023 in PNAS, with doi: 10.1073/pnas.2308489120

Leaving On a Jet Plane Without the Brain in Luggage Compartment was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

Unexpected dietary behavior in snow leopards

Big felines may not know Scarborough Fair, but felids such as alpine cats — both in the wild and in captivity — do eat plants despite their classification as carnivores. In particular, Panthera uncia — or snow leopards — seem to have a preference for a specific plant species despite normally being unsuited for a herbivorous diet.

Although some proposed hypotheses include supplemental nutrition or hydration, self-medication for diseases, and digestive aid, the precise reason why these felids consume plants has remained a mystery.

Now, a team of researchers from Kyoto University has identified the DNA of prey animals and plants within the feces of snow leopards. The plant genus Myricaria appeared the most frequently in metabarcoding analysis of 90 fecal samples of wild snow leopards collected in the Kyrgyz Republic.

“Given that felids are essentially carnivores, we were surprised to see a higher frequency of Myricaria in samples with little or no trace of prey animal DNA, suggesting that the plant is consumed by snow leopards when they are hungry,” explains team leader Kodzue Kinoshita of KyotoU’s Graduate School of Asian and African Area Studies in Ecology and Environment.

In addition to snow leopard feces, Kinoshita’s team also collected 36 samples from other mammals in the alpine habitat of Kyrgyzstan’s Sarychat-Ertash Nature Reserve, marking the first study evaluating the relationship between prey animals and plants in felid feces.

In previous studies of 41 extant felid species, researchers found plants in the feces of 24 species. Among these, snow leopard feces contained up to 45% Myricaria. However, the inconclusive results fell short of determining whether Myricaria was more present in snow leopard feces than other plants or whether the Myricaria phenomenon was unique to snow leopards.

The team’s investigation, which applied a molecular-based approach, has provided insight into Myricaria’s significant abundance in snow leopard feces and the plant’s noticeable absence in other mammalian feces. In addition, feces containing this plant often did not contain prey animals.

“Through our innovative research, we anticipate providing insight into improved captive environments and more suitable conservation plans for the snow leopard,” concludes Kinoshita.

The paper “Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard” appeared on 29 May 2024 in Royal Society Open Science, with doi: 10.1098/rsos.240132

Big Cats Chant Parsley, Sage, Rosemary, and Thyme? was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

Doubts about whether micronuclei activate cGAS-STING pathway

Kyoto, Japan — Cells possess an innate immune system that defends against invasive pathogens such as bacteria and viruses. Previous studies have mapped out the cytoplasmic cGAS-STING pathway in the cytoplasm, known for responding to foreign nucleic acids, such as double-stranded DNA.

Micronuclei — or MN, abnormal intracellular structures containing the cell’s DNA — have also been suspected of triggering the pathway. However, no conclusive evidence exists of pathway activation by MN-induced cyclic GMP-AMP synthase, or cGAS.

Now, Kyoto University and the AIRC Institute of Molecular Oncology, or IFOM, have collaborated to develop the reporter cell line Fusion Visualization system 2 — FuVis2 — designed to help researchers visualize cellular nuclei with chromosome fusion and resulting MN. Using FuVis2, they examined whether MN influences the cGAS-STING response in live cells, where STING refers to stimulators of interferon genes.

“Our findings suggest cGAS more commonly recognizes MN during cell division without activating STING in the following cell cycle, contrary to the existing theory that cGAS-bound MN leads to STING activation,” says lead author Makoto Hayashi at the IFOM-KU Joint Research Laboratory at KyotoU’s Graduate School of Medicine.

The team also showed that cGAS-STING activation by gamma irradiation leads to mitochondrial DNA leakage into the cytoplasm and is not associated with MN formation. The observed MN inactivity against innate immune responses may suggest chromosomal abnormalities with severe consequences.

Radiation-generated MN had been reported to activate the cGAS-STING pathway, so the researchers began using MN as a model for cGAS activation.

“However, we were excited to obtain the opposite results,” says Yuki Sato at KyotoU’s Graduate School of Biostudies.

Previous correlative results have also suggested that an MN-mediated innate immune response may drive cellular senescence and suppress cancer. However, Hayashi’s team now feels the need to revisit this model.

“Given that these findings were derived specifically from the human colon cancer cell type HCT116, we should also conduct further analyses across different cell types and species before establishing theories about the MN-activated pathway,” concludes Hayashi.

The paper “Micronucleus is not a potent inducer of the cGAS/STING pathway” appeared on 2 February 2024 in Life Science Alliance, with doi: 10.26508/lsa.202302424

Sting operation out of gas was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

Cancer, the second leading cause of death worldwide, is more likely to respond to effective treatment if identified early before metastasizing, resulting in a greater probability of surviving.

Some rare cancers outsmart human interventions and metastasize before being detected. Alveolar soft-part sarcoma, or ASPS, accounts for only 0.01% of all cancers. Although ASPS grows slowly, it can spread quickly in the body, dodging conventional chemotherapy.

To understand the cancer’s angiogenic — blood vessel growth — mechanism, researchers have relied on models using immunocompromised animals engrafted with patient-derived tumor samples. However, conventional methods restrict researchers with ethical issues and provide no information about molecular mechanisms such as intercellular interactions.

Now, a team of researchers, including Kyoto University, has developed the first ASPS-on-a-chip, which closely mimics the microenvironment during tumor vessel formation.

“Our microfluidic co-culture vasculature chip should give us insight into the angiogenic mechanism and possible strategies for stopping tumor growth in ASPS patients,” says lead author Surachada Chuaychob of KyotoU’s Department of Micro Engineering (now at KyotoU’s Institute of Advanced Energy).

The team designed this tumor-mimicking chip to reproduce the natural functions of human endothelial cells and pericytes to form blood capillaries in the initial stage of ASPS in vitro.

“We discovered that blood vessels with pericytes, also known as angiogenic sprouts, can be induced with improved results in a 3D spheroid made entirely of ASPS tumor cells on a chip,” reveals team leader Ryuji Yokokawa at KyotoU’s Department of Micro Engineering.

“The in vitro model demonstrates the cell-to-cell interactions leading to ASPS angiogenesis, which confirms previous in vivo results,” explains co-author Takuro Nakamura at Tokyo Medical University.

“Our study is also crucial in highlighting the critical roles of Rab27a and Sytl2 proteins in intracellular trafficking and verifying cell-to-cell interactions in ASPS angiogenesis,” adds Miwa Tanaka at the Japan Foundation for Cancer Research.

Yokokawa’s team anticipates applying their ASPS-on-a-chip model as a screening tool for developing new drugs by suppressing intracellular trafficking proteins to decrease ASPS angiogenesis.

“Our microfluidic co-culture vasculature chip could advance our study of angiogenic mechanisms in different cancers and development of personalized treatments,” notes Yokokawa.

If you can’t beat’em, then mock’em was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.

Connecting the dots to shape growth

Key signal protein directs lung curvature in mice

Kyoto, Japan — Branching patterns are prevalent in our natural environment and the human body, such as in the lungs and kidneys. For example, specific genes that express growth factor proteins are known to influence the development of the lungs’ complex branches. Still, until now the mechanics behind this phenomenon have remained a mystery.

Kyoto University researchers have unveiled a regulatory system linking signal, force, and shape in mouse lung structure development. The team recognized that the signal protein ERK plays an active role in causing growing lung tissue to curve.

“ERK signals the cell tissue to stretch outward to smoothen its curve,” says Tsuyoshi Hirashima, formerly of KyotoU’s Graduate School of Biostudies and now at the National University of Singapore’s Mechanobiology Institute.

As if choreographed, a mix of chemical signals triggers the cellular mechanics of the lungs of a mouse embryo, resulting in the development of intricate branching patterns.

Mechanobiology has gained increasing attention in recent years, focusing on cell- and tissue-generated forces, intracellular signaling, and their combined interactions with geometric factors that influence morphogenesis.

“ERK’s surprisingly precise signaling response to lung tissue curvature was enlightening. It suggests an elegantly more nuanced developmental orchestration than previously thought,” reflects Hirashima.

Utilizing advanced microscopic imaging techniques, Hirashima’s team observed how ERK behaves in developing lungs in real time by combining a fluorescent biosensor — for quantifying the ERK activity in living cells — with two-photon microscopy, which captures tissue cell and molecular activities in 3D.

Results showed that ERK mediates curvature sensing and force generation in epithelial cells, causing a negative feedback loop and a repetitive branching pattern.

“We are particularly interested in exploring how disruptions in this signal-force-shape system might contribute to physiological abnormalities or diseases,” says Hirashima.

These ideas may apply to the developmental processes of other organs and the formation of mouse lungs, a realization that calls for further exploration of fundamental principles.

“Ultimately, our findings offer a deeper understanding of the novel principles of biological regulatory systems, with promising applications in regenerative medicine and organoid research,” concludes Hirashima.

The paper “ERK-mediated Curvature Feedback Regulates Branching Morphogenesis in Lung Epithelial Tissue” appeared on 15 January 2024 in Current Biology, with doi: 10.1016/j.cub.2023.12.049

Connecting the Dots to Shape Growth was originally published in Unreleashed on Medium, where people are continuing the conversation by highlighting and responding to this story.