A novel miniTurbo knock-in mouse reveals a protein interaction network of USP46 in the brain.

Uncovering protein interaction networks in vivo is essential for understanding physiological and pathological processes. Here, we report the generation of a novel knock-in mouse model expressing miniTurbo, a highly active biotin ligase, fused to the endogenous Usp46 gene. This model enables proximity-dependent biotinylation (BioID) of USP46-associated proteins in the brain.

Long-term live imaging, cell identification and cell tracking in regenerating crustacean legs.

High-resolution live imaging of regeneration presents unique challenges due to the nature of the specimens (large mobile animals), the duration of the process (spanning days or weeks), and the fact that cellular resolution must be achieved without damage caused by lengthy exposures to light. Building on previous work that allowed us to image different parts of the process of leg regeneration in the crustacean , we present here a method for live imaging that captures the entire process of leg regeneration, spanning up to 10 days, at cellular resolution. Our method includes (1) mounting and long-term live imaging of regenerating legs under conditions that yield high spatial and temporal resolution but minimise photodamage, (2) fixing and in situ staining of the regenerated legs that were imaged, to identify cell fates, and (3) computer-assisted cell tracking to determine the cell lineages and progenitors of identified cells.

Computational mechanisms of neuroimaging biomarkers uncovered by multicenter resting-state fMRI connectivity variation profile.

Resting-state functional connectivity (rsFC) is increasingly used to develop biomarkers for psychiatric disorders. Despite progress, development of the reliable and practical FC biomarker remains an unmet goal, particularly one that is clinically predictive at the individual level with generalizability, robustness, and accuracy. In this study, we propose a new approach to profile each connectivity from diverse perspective, encompassing not only disorder-related differences but also disorder-unrelated variations attributed to individual difference, within-subject across-runs, imaging protocol, and scanner factors.

Toward improved AAV gene therapies for retinal disorders: challenges and advances.

Adeno-associated virus (AAV) vectors have transformed the landscape of in vivo gene therapy, with retinal diseases emerging as a major area of progress. The eye offers unique advantages as a therapeutic target: it is accessible, compartmentalized, and relatively immune-privileged, allowing localized delivery with reduced systemic effects. The landmark 2017 approval of the first AAV-based gene therapy for an inherited retinal disorder sparked a surge of clinical trials using AAV vectors - underscoring their potential for treating genetic eye diseases.

Multistate Structure Determination and Dynamics Analysis Reveals a Unique Ubiquitin-Recognition Mechanism in Ubiquitin C-terminal Hydrolase.

Despite accumulating evidence that protein dynamics is indispensable for understanding the structural basis of biological activities, it remains challenging to visualize the spatial description of the dynamics and to associate transient conformations with their molecular functions. We have developed a new NMR protein structure determination method for the inference of multistate conformations using multiple types of NMR data, including paramagnetic NMR and residual dipolar couplings, as well as conventional NOEs. Integration of these data in the structure calculation permits delineating accurate ensemble structures of biomacromolecules.

Positron Emission Tomography-Based Pharmacokinetics of mRNA-Lipid Nanoparticles: A Study Quantifying the ApoE and Macrophage Contribution.

It is important to clarify the pharmacokinetics of mRNA-loaded lipid nanoparticles (mRNA-LNPs), which have attracted attention as new pharmaceutical modalities for vaccines and therapeutic agents against various diseases. Positron emission tomography (PET) is expected to provide data to ensure the pharmacokinetics of mRNA-LNPs early after administration in detail, especially because of its high temporal resolution. In this study, we have developed a method for the preparation of Cu-labeled mRNA-LNPs by an approach via hybridization of short oligonucleotides to the 3' UTR region of mRNA, and conducted PET pharmacokinetic studies in normal and functionally deficient mice after intravenous and intramuscular administration, which mainly yielded the following findings.

Synthetic torpor: advancing metabolic regulation for medical innovations.

Torpor is a naturally occurring state of metabolic suppression that enables animals to adapt and survive extreme environmental conditions. Inspired by this adaptation, researchers have pursued synthetic torpor-an artificially induced, reversible hypometabolic state with transformative medical potential. Achieving synthetic torpor has been pursued for over a hundred years, with earlier work focused on identifying drugs for systemically suppressing metabolism.

Optimization of Malonyl Coenzyme A Biosensors in a Reconstituted Cell-Free System for Detecting Acetyl-CoA Carboxylase Activity.

Malonyl coenzyme A (malonyl-CoA) is a key precursor in the biosynthesis of fatty acids and polyketides, critical for industrial applications such as biofuel and pharmaceutical productions. Optimizing acetyl-CoA carboxylase (ACC), the enzyme that converts acetyl-CoA to malonyl-CoA, is essential for advancing metabolic engineering. Effective biosensors that detect malonyl-CoA levels are vital for high-throughput screening and directed evolution of ACC.

High-Fat Diet-Fed Kcnq1 Mutant Mice Have Reduced Pancreatic β-Cell Mass via Gene-Environment Interaction.

Background: The potassium voltage-gated channel subfamily Q member 1 (KCNQ1) gene has recently received much attention as a candidate susceptibility gene for type 2 diabetes mellitus, especially in Asian populations. We previously reported that Kcnq1 mutant mice exhibit reduced insulin secretion and hyperglycemia due to a decrease in pancreatic β-cell mass. Through in vivo and in vitro analyses, we ascertained that this mechanism is the result of the downregulation of the non-coding RNA 'Kcnq1ot1,' which is expressed in the paternal allele of the Kcnq1 gene region, causing an increase in the expression of the cell cycle inhibitor cyclin dependent kinase inhibitor 1C (Cdkn1c).

Comparative analysis of autofluorescence spectra in a filet of three fish species during chilled storage for raw consumption.

Recent advances in fish freshness evaluation rely on a combination of optical imaging and artificial intelligence due to their applicability to non-invasive and non-destructive measurements. Using trout salmon, red sea bream, and Japanese amberjack, we investigated the feasibility of using autofluorescence spectroscopy, influenced by biochemical reactions, to assess the freshness of fish filets. Spectral analyses using principal component analysis and curve-fitting revealed considerable differences among species.

Hidden Markov Model-Based Behavioral Classification Reveals Visual Function Recovery After Retinal Organoid Transplantation in Mice.

Retinal degenerative diseases cause irreversible vision loss due to photoreceptor degeneration. Retinal organoid transplantation offers a promising strategy for restoring vision, but assessing functional recovery remains challenging. Standard visual function tests provide binary or coarse measures that do not fully capture how visual input influences natural behavior.

Protein design of two-component tubular assemblies similar to cytoskeletons.

Recent advances in protein design have ushered in an era of constructing intricate higher-order structures. Nonetheless, orchestrating the assembly of diverse protein units into cohesive artificial structures akin to biological assembly systems, especially in tubular forms, remains elusive. To this end, we develop a methodology inspired by nature, which utilises two distinct protein units to create unique tubular structures under carefully designed conditions.

Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms.

Sex determination has been investigated across vertebrate lineages to reveal the stepwise evolution of sex chromosomes and the diversity of responsible molecular mechanisms. However, these studies rarely include cartilaginous fishes, which diverged from the other vertebrates 450 Mya, hindering the comprehensive view of vertebrate sex determination. Here, we produced chromosome-scale genome assemblies of egg-laying shark species and comparatively investigated genome sequences and transcriptome profiles across diverse cartilaginous fishes.

Reorganization of Social Representations in the Insular Cortex During Conspecific Familiarization and Discrimination.

The familiarity of socially interacting peers markedly impacts behavior. However, the neuronal representations that distinguish familiar from novel conspecifics within the social brain network are not fully understood. Following our previous findings that neurons in the agranular insular cortex represent ongoing social interactions, we monitored the activity of neurons in the agranular insular cortex using microendoscopic calcium imaging in mice during social recognition memory and linear chamber social discrimination tasks.

GloBIAS: strengthening the foundations of BioImage Analysis.

There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of biological images. Turning these data into scientific discoveries requires people with effective data management skills and knowledge of state-of-the-art image processing and data analysis, in other words, BioImage Analysts. The Global BioImage Analysts' Society (GloBIAS) aims to enhance the profile of BioImage Analysts as a key role in science and research.

Comprehensive Identification of Proteins Interacting with Long Non-Coding RNA TUG1 in R-Loop Regulation.

Long non-coding RNAs (lncRNAs) regulate a wide array of cellular processes through interactions with RNA-binding proteins (RBPs). Taurine Upregulated Gene 1 (TUG1) is a lncRNA that is overexpressed in many types of cancer and has been implicated in resolving R-loops, thereby maintaining genomic integrity. However, the full spectrum of its protein interactions and stress-responsive dynamics remains unclear.

OpenCafeMol: A coarse-grained biomolecular simulator on GPU with its application to vesicle fusion.

There has been an increasing demand for longer-timescale molecular dynamics (MD) simulations of larger biomolecular systems. To meet these demands, using the C++ API of OpenMM, we developed a fast and flexible MD software, OpenCafeMol, for residue-resolution protein and lipid models that shows high performance on graphics processing unit (GPU) machines. We validated OpenCafeMol for folding small proteins, lipid membrane dynamics, and membrane protein structures.

Characterizing primary and secondary senescence in vivo.

There is robust evidence that senescence can be propagated in vitro through mechanisms including the senescence-associated secretory phenotype, resulting in the non-cell-autonomous induction of secondary senescence. However, the induction, regulation and physiological role of secondary senescence in vivo remain largely unclear. Here we generated senescence-inducible mouse models expressing either the constitutively active form of MEK1 or MKK6 and mCherry, to map primary and secondary senescent cells.

Acquisition of auditory discrimination mediated by different processes through two distinct circuits linked to the lateral striatum.

The striatum, the central hub of cortico-basal ganglia loops, contains functionally heterogeneous subregions distinguished by the topographic patterns of structural connectivity. These subregions mediate various processes of procedural learning. However, it remains unclear when and how striatal subregions engage in the acquisition of sensory stimulus-based decision-making.

Growth phase diets diminish histone acetyltransferase Gcn5 function and shorten lifespan of Drosophila males.

The nutritional environment in early life, referred to as the nutrition history, exerts far-reaching health effects beyond the developmental stage. Here, with Drosophila melanogaster as a model, we fed larvae on diets consisting of a variety of yeast mutants and explored the resulting histories that impacted adult lifespan. A larval diet comprised of yeast nat3 KO shortened the lifespan of male adults; and remarkably, this diet diminished the function of histone acetyltransferase Gcn5 in larvae.

Transplantation of vascularized cardiac microtissue from human induced pluripotent stem cells improves impaired electrical conduction in a porcine myocardial injury model.

Objective: To demonstrate that the transplantation of human induced pluripotent stem cell (hiPSC)-derived vascularized cardiac microtissue (VCM) can improve conduction disturbances after myocardial injury (MI).

Methods: We prepared cell sheet-shaped VCM with hiPSC-derived cardiomyocytes and vascular cells using dynamic rocking culture. We induced MI via epicardial cryoablation in immunosuppressed crown minipigs (VCM and sham groups; n = 3) and transplanted the VCMs immediately after MI induction.

Epithelial cell chirality emerges through the dynamic concentric pattern of actomyosin cytoskeleton.

The chirality of tissues and organs is essential for their proper function and development. Tissue-level chirality derives from the chirality of individual cells that comprise the tissue, and cellular chirality is considered to emerge through the organization of chiral molecules within the cell. However, the principle of how molecular chirality leads to cellular chirality remains unresolved.

IFNγ-inducible Gbp4 and Irgb6 contribute to experimental cerebral malaria pathology in the olfactory bulb.

Cerebral malaria (CM) is a severe and often fatal complication of infection. Although much progress has been made in understanding CM, the precise pathogenesis remains elusive. The olfactory bulb (OB) has emerged as a critical site of immunopathology in experimental cerebral malaria (ECM) models, but its contribution to disease progression is not fully understood.

Meeting Report: The First Evo-Devo Young Researchers Meeting.

The official poster for the First Evo-Devo Young Researchers Meeting. It features the meeting title, themes ("Evo-Devo so far" and "Evo-Devo in the future"), invited speakers, program highlights, and logistical details. The content is written in Japanese.

Orbitofrontal cortex influences dopamine dynamics associated with alloparental behavioral acquisition in female mice.

Maternal behaviors, which are crucial for the survival of mammalian infants, require the coordinated operation of multiple brain regions to process infant cues, make decisions, and execute motor plans. Although these processes likely demand higher cognitive functions, the prefrontal areas that regulate limbic parental programs remains poorly understood. Here, we show that the orbitofrontal cortex (OFC) excitatory projection neurons promote alloparental caregiving behaviors in female mice.