Life Science Institute

Tissue clearing has been widely used for fluorescence imaging of fixed tissues, but its application to live tissues has been limited by toxicity. Here we develop minimally invasive optical clearing media for fluorescence imaging of live mammalian tissues. Light scattering is minimized by adding spherical polymers with low osmolarity to the extracellular medium. A clearing medium containing bovine serum albumin (SeeDB-Live) is compatible with live cells, enabling structural and functional imaging of live tissues, such as spheroids, organoids, acute brain slices and the mouse brains in vivo. SeeDB-Live minimally affects neuronal electrophysiological properties and sensory responses in vivo, and facilitates fluorescence imaging of deep cortical layers in live animals without detectable toxicity to neurons or behavior. We further demonstrate its utility to epifluorescence voltage imaging in acute brain slices and in vivo preparations. Thus, SeeDB-Live expands both the depth and modality range of fluorescence imaging in live mammalian tissues.

The gut microbiome is a highly dynamic ecosystem, yet its temporal organization remains poorly understood because microbiome sampling is typically limited to sparse time points. To overcome this challenge, we developed an automated device to enable continuous fecal sampling from individual mice at minute- to hour-scale resolution. Combining full-length 16S rRNA amplicon sequencing with a limited set of long-read metagenomic references, we economically reconstructed genome- and function-level trajectories at high temporal resolution. Automated hourly sampling over 14 consecutive days enabled phase analysis, revealing collective synchronization of taxa partitioned by carbohydrate utilization strategies between day and night, with microbial taxa and functional genes showing reproducible temporal succession across mice. Perturbations such as cage transfer or antibiotic treatment transiently disrupted this functional synchronization, followed by recovery toward a coherent dynamical state. This system and analytic frameworks will enable us to explore rapid microbiome dynamics in health and disease.

Abstract The spatial arrangement of cells is fundamental to the mechanical and functional integrity of three-dimensional (3D) tissues, yet engineering spatially well-controlled tissue architectures remains challenging. Here, we computationally investigated how layered tissue architectures can be designed by modulating cell-cell interfacial tension. We performed simulations using a 3D vertex model and systematically varied interfacial tension magnitudes. The simulations generated a range of layered tissue architectures, including planar monolayers, bilayers, and structurally stratified states. In homogeneous cell populations, increasing interfacial tension drove transitions from monolayer to structurally stratified configurations. In heterogeneous populations, differential interfacial tensions induced out-of-plane cell sorting and the formation of compositionally sorted multilayers. Moreover, a recursive tension design strategy enabled hierarchical organization of multiple cell types into separate layers. Notably, this recursive scheme uses only two tension levels (high vs. low) assigned across interfaces and can, in principle, be extended to specify layered architectures with an arbitrary number of layers. Together, these results identify cell-cell interfacial tension as a tunable mechanical parameter for regulating layered tissue architecture and provide design principles for layered tissue engineering and regenerative medicine.

The Core-Mantle Boundary (CMB) is a critical interface influencingEarth’s thermal and chemical evolution. Among the various featuresin the CMB region, the D” seismic reflector—located approximately300 km above the CMB—is of particular interest. Mineral physicslinks this reflector, which generates distinct P- and S-wave reflec-tions and increases S-wave velocity by 2–3 % and P-wave velocity by0.5–2 %, to a phase transition from bridgmanite to post-perovskite.If these reflections stem from the phase transition, variations in re-flector depth directly reflect lateral changes in temperature and rockcomposition near the CMB. In this study, we modelled phase transi-tions across a range of temperature–composition conditions to pro-duce synthetic seismograms, demonstrating how these factors influ-ence velocity jumps, reflector depth, and reflectivity. We also com-piled data from over 65 previous studies measuring the D” reflector’sdepth, addressing the lack of a coherent global map since the identifi-cation of post-perovskite in 2004. Our compilation shows that shal-lower reflector depths are found in seismically fast (cold) regions,while deeper reflectors are found in seismically slow (hot) regions,consistent with theoretical predictions of post-perovskite occurrence.This global map establishes a consistent framework for comparingphase transition models with seismic observations.

Hexaboraheptacene (B6-hept), featuring a periodic arrangement of boron atoms, together with its shorter homologues tetraborapentacene (B4-pent) and diboraanthracene (B2-ant), were synthesized via cyclocondensation of o-bis(dihydroboryl)arenes. The reactive boron centers are effectively protected by 2,4,6-triisopropylphenyl (Tip) groups, enabling handling under ambient conditions. As the number of boron bridges increases, the electron-accepting ability as well as the multistep reversible redox properties are progressively enhanced. B6-hept exhibits pronounced dual fluorescence in solution, in which relative intensities depend on the excitation wavelength and solvent viscosity. DFT calculations suggest that this phenomenon originates from two interconvertible conformers, namely, the bent-zigzag and twisted forms, which result from a delicate balance between the extended π-system and the steric demands of the Tip groups. This interpretation is supported by the fact that B4-pent displays only weak dual emission, while B2-ant shows none. This study not only introduces a new class of heteroacenes with potential applications in optoelectronics and electrocatalysis, but also provides insight into steric-design strategies for tuning the conformational landscapes of boron-containing π-systems.

Organic-inorganic hybrid layered porous materials enabling triplet-triplet annihilation upconversion (TTA-UC) were developed by integrating anthracene-based emitters and metal-complex sensitizers within zeolitic nanospace. Diphenylanthracene (DPA) units were covalently anchored between MWW-type layers via thiol-ene click chemistry, forming organic pillars that generated ordered interlayer micropores, confirmed by XRD and N2 adsorption. Incorporation of cationic chromophores and Pt(octaethylporphyrin) [Pt(OEP)] enabled efficient intermolecular energy transfer. Upon 535 nm excitation, Pt(OEP)-loaded samples exhibited phosphorescence at 650 nm and upconverted emission at 400-500 nm. This work highlights a rational strategy for tuning nanoscale photochemical behavior via host-guest engineering in layered hybrid systems.

Designing synthetic biomolecular condensates, or membraneless organelles, offers insights into the functions of their natural counterparts and is equally valuable for cellular and metabolic engineering. Choosing E. coli for its biotechnological relevance, we deploy RNA nanotechnology to design and express non-natural membraneless organelles in vivo. The designer condensates assemble co-transcriptionally from branched RNA motifs interacting via base-pairing. Exploiting binding selectivity, we express orthogonal, non-mixing condensates, and by embedding a protein-binding aptamer, we achieve selective protein recruitment. Condensates can be made to dissolve and reassemble upon thermal cycling, thereby reversibly releasing and re-capturing protein clients. The synthetic organelles are expressed robustly across the cell population and remain stable despite enzymatic RNA processing. Compared with existing solutions based on peptide building blocks or repetitive RNA sequences, these nanostructured RNA motifs enable algorithmic control over interactions, affinity for clients, and condensate microstructure, opening further directions in synthetic biology and biotechnology.

Abstract Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses 1–5 . However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes 6–10 . Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications 11–16 . Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels 17,18 . Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.

Multiple myeloma remains a therapeutic challenge despite recent advances with proteasome inhibitors, immunomodulatory drugs (IMiDs), and monoclonal antibodies. Among new approaches, the combination of IMiDs and histone deacetylase inhibitors has shown promise in relapsed or refractory multiple myeloma. Here, we elucidate the molecular basis of their synergy and its role in overcoming drug resistance in myeloma cells. We demonstrate that these agents converge to downregulate the master oncogene MYC, resulting in synergistic cytotoxicity. Importantly, this effect persists even in models intrinsically resistant to IMiDs, where the canonical IKZF1/3-IRF4/MYC axis is functionally uncoupled. In this context, the combination engages an alternative ARID2-MYC axis, mediated by the synergistic downregulation of the IMiD neosubstrate ARID2. This finding highlights the functional relevance of IMiD's inherent polypharmacology in circumventing primary resistance mechanisms at the cellular level. Together, our results identify the ARID2-containing PBAF complex as a critical vulnerability in resistant myeloma cells and provide a mechanistic rationale for designing combination strategies that co-target this complex, with the potential to enhance therapeutic efficacy by overcoming drug resistance.