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A bifunctional optical reporter for tracking estrogen response dynamics in neurons

Estrogens are inherently dynamic signaling molecules whose fluctuations induce profound shifts in physiology and behavior. However, methods for tracking the dynamics of estrogen action in vivo are limited and not tissue-specific, making it difficult to directly relate dynamics to ongoing physiological, behavioral, and neural changes. Traditionally, estrogen sensitive cells have been identified by metrics such as receptor expression or radioactive ligand binding, but these measures do not capt...

— Cara, A. L., Guthman, E. M., Mishra, A., Hall, A. L., Yokoyama, S., Sandoval, N. P., Gregg, I. P., Aghi, K., Soma, K. K., Correa, S. M., Falkner, A. L., van Veen, E. 2025-12-14 00:00:00

Satellite microglia gate neuronal excitability by shielding inhibitory synapses in adult brain

Microglia, the primary immune cells of the central nervous system, are known for sculpting excitatory neural circuits via dynamic processes. However, their role in modulating inhibitory synaptic connections in adulthood remains largely unexplored. In this study, we identified an underappreciated microglia subpopulation, satellite microglia with physical soma-soma contact with neurons, that reshape inhibitory circuit connectivity and gate neuronal activity by shielding inhibitory synapses in t...

— Zhao, S., Fei, M., Zheng, J., Christensen, T. A., Kleidonas, D., Liang, Y., Qi, F., Haruwaka, K., Wang, L., Worrell, G. A., Nguyen, A. T., Wu, L.-J. 2025-12-14 00:00:00

Differential Regulation of APOE4-Mediated Astrocytic Lipid Metabolism by BMP Signaling Exacerbates Alzheimers Disease Pathologies in Neurons

The two greatest risk factors for Alzheimers Disease (AD) are aging and Apolipoprotein E4 (APOE4) polymorphism, yet how these factors interact remain unclear. In this study, we investigate how bone morphogenetic protein (BMP) signaling, which increases with age, contributes to APOE4-induced lipid metabolic dysfunctions using induced-pluripotent stem cell (iPSC)-derived astrocytes and cocultured neurons. Surprisingly, BMP signaling differentially altered lipid droplet formation, cholesterol sy...

— Linden, A. K., Affaneh, A., Aylward, A., Wong, Y., Kessler, J. A., Peng, C.-Y. 2025-12-14 00:00:00

δ2-Protocadherins organize parallel indirect basal ganglia circuits

The basal ganglia (BG) contain multiple parallel neural circuits, each of which may control different behaviors. However, how the distinct parallel BG circuits are molecularly organized is not known. Here we show that two {delta}2-protocadherins (PCDHs), PCDH17 and PCDH10, which are homophilic cell-adhesion molecules, establish and define two distinct indirect BG circuits that regulate different behaviors. PCDH17 and PCDH10 are expressed in a complementary expression pattern in the BG, anatom...

— Hoshina, N., Boeckers, J. M., Johnson-Venkatesh, E. M., Hoshina, M., Matsumoto, K., Das, A., Rally, V. R., Sant, J., Inoue, T., Umemori, H. 2025-12-15 00:00:00

Cross-Platform Calibration of Epigenetic Age Between the EPICv2 and MSA Arrays

Epigenetic clocks are regression models that predict biological age based on the DNA methylation patterns. They are developed using DNA methylation array data; however, systematic differences in the predicted values between the Infinium Methylation Screening Array (MSA) and Infinium MethylationEPIC v2.0 BeadChip (EPICv2) platforms have not been evaluated. We quantified the systematic differences between the MSA and EPICv2 arrays for six major epigenetic clocks (Horvath, Hannum, PhenoAge, Grim...

— Tomo, Y., Shoji, T., Nakaki, R. 2025-12-14 00:00:00

Comparing the evolvability of an ancestrally reconstructed and modern adenylate kinase

Directed evolution revolutionized the field of protein engineering by establishing a highly customizable framework to produce enzymes with enhanced catalytic power for a wide range of functions. However, modern enzymes subjected to directed evolution frequently plateau in improvement due to entrapment in local maxima on their fitness landscapes. Ancestral enzymes have been proposed as superior starting points for directed evolution due to their increased thermostability. Here we propose and e...

— Patterson, M., Ludewig, H., Wilson, C., Woldring, D. R., Kim, C., Using, A., Irvin, J., Theobald, D. L., Kern, D. 2025-12-14 00:00:00

Identification of Vector Organisms and Their Carried Pathogens by Metagenomic Sequencing

Vector surveillance is vital for public health, yet traditional methods often face limitations. This study assessed the use of metagenomic sequencing for analyzing mosquitoes, cockroaches, flies, and rodents from Zhongshan, China. The results revealed a high concordance between metagenomic and Sanger sequencing for species identification (Kappa = 0.667, P = 0.011). Metagenomic analysis identified vector-specific dominant bacteria, including Wolbachia in mosquitoes, Blattabacterium sp. in cock...

— Wu, S., Li, Z., Qiu, D., Yue, Q., Liu, D., Wei, X., Li, T., Qian, Y., Cheng, X., Wang, H.-B., Chen, J. 2025-12-14 00:00:00

YME1L-dependent regulation of mitochondrial Ca2+ transport: a role for mitochondrial uptake protein 1 (MICU1) in nutrient sensing

Mitochondrial calcium uptake via the mitochondrial calcium uniporter complex (MCUc) is tightly regulated by gatekeeper proteins such as MICU1 and MICU2. While long-term nutritional interventions have been shown to remodel the MCUc, its short-term regulation during postprandial transitions and acute nutrient stress remains unclear. Here, we demonstrate that non-gated MCUc increases in the postprandial liver due to a transient loss of mature MICU1 (m-MICU1), accompanied by changes in its precur...

— Serna, J. D., D Angelo, D., Ohya, G., Rizzuto, R., Kowaltowski, A. J., Raffaello, A. 2025-12-14 00:00:00

Ehrlich occupancy time: Beyond koff to a complete residence time framework

Drug-target occupancy time--the cumulative duration a target remains bound--critically influences therapeutic efficacy. While Copeland's widely-used residence time (1/koff) emphasizes dissociation kinetics, it neglects association rates, rebinding events, and drug elimination that affect in vivo outcomes. Returning to Paul Ehrlich's 1913 principle that drugs act only when bound ("Corpora non agunt nisi fixata"), we develop a mathematically rigorous framework defining Ehrlich occupancy time as...

— Eilertsen, J., Schnell, S., Walcher, S. 2025-12-14 00:00:00

Automatic binding of basic sensory features requires consciousness

Conscious awareness requires establishing coherent percepts. Yet, whether consciousness is necessary for initiating the integration of basic sensory features remains unclear. Competing theories implicate distinct functional regimes of consciousness in the process of feature binding and creating conscious percepts. We used a novel multi-feature oddball paradigm with intracranial stereo-electroencephalography (sEEG) recordings in awake and anesthetized states to investigate the functional bound...

— Han, Z., Zhu, H., Chu, Q., Wu, Y., Chen, X., Wang, Y., Li, S., Teng, X., Wong, P., Yao, C., Tian, X. 2025-12-14 00:00:00

Going Against the Grain: Investigating the C4 Wheat Hypothesis with Spatial Transcriptomics

The possibility of a C4 photosynthetic pathway present in the developing grain of wheat, a C3 plant, has been the source of scientific debate. Wheat is critical to food security and may benefit greatly from the biological advantages conferred by C4 photosynthesis under heat and drought stress. Therefore, significant research has gone towards engineering wheat to use C4 biochemistry, resulting in the discovery of a unique photosynthetic pathway in the grain that has been suggested to be C4 spe...

— Millsteed, T., Kainer, D., Sullivan, R., Sun, X., Li, K. L., Mao, L., Macdonald, A., Henry, R. J. 2025-12-14 00:00:00

Unexpected functional role of the transactivation domain for nuclear import of STAT5

Signal transducer and activator of transcription 5 (STAT5) is a key transcriptional regulator acting downstream of hematopoietic cytokines and hormones, such as erythropoietin (Epo), thrombopoietin or prolactin. STAT5-mediated gene regulation involves tyrosine phosphorylation at cytokine receptors and subsequent nuclear import. We studied STAT5 nucleocytoplasmic shuttling via live-cell imaging of fluorescent mutants in STAT5-/- HeLa EpoR cells. Unexpectedly, STAT5 mutants lacking the transact...

— Ernst, S., Borgen-Moller, M., Kuster, A., Schurse, H., Muller-Newen, G. 2025-12-14 00:00:00

Microglia and its P2RY12 Receptors Regulate Seizure Severity

Microglia have emerged as possible regulators of seizures with previous approaches employed being insufficiently selective of microglial-specific contributions. To more definitely determine microglial roles in seizure severity, we used the recently developed genetic microglial-deficient Csf1r{Delta}FIRE/{Delta}FIRE (FIRE KO) mouse model. In this model, mice lack microglia but retain brain border associated macrophages (BAMs). Using two experimental seizure paradigms with either a chemoconvuls...

— Fremuth, L. E., Gibbs-Shelton, S., Perez-Reyes, E., Gaykema, R., Eyo, U. B. 2025-12-14 00:00:00

Efficient RNA Folding Simulation via a Structure-Based Single-Site-Per-Nucleotide Model

Computational modeling of large RNA structures and their dynamics is essential for uncovering the molecular mechanisms underlying various genomic processes and RNA-regulated cellular functions. Residue-resolution modeling is an effective approach for simulating large biomolecular structures while preserving essential sequence and structural features presented in atomic structures. Here, we implemented a structure-based single-site-per-nucleotide (SSPN) RNA model using the GPU-accelerated Open...

— Thornton, T., Lin, X. 2025-12-14 00:00:00

A mechanistic free-energy model explains and predicts sequence- and context-dependent CRISPR-Cas9 activity

Accurate prediction of CRISPR-based gene editing remains challenging since existing models often fail to generalize across experimental and cellular contexts. We introduce CRISPRzip, a mechanistic kinetic model that quantitatively links nucleotide sequence and environmental conditions to target interrogation. The model describes R-loop formation as movement through a sequence-dependent free-energy landscape, combining nearest-neighbor nucleic-acid energetics with protein-mediated contribution...

— Offerhaus, H. S., Jaskovikaite, I., Jones, S. K., Depken, M. 2025-12-14 00:00:00

Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling

SH2 domains are critical mediators of cellular signaling, although the molecular mechanisms by which they bind their phosphopeptide ligands remain incompletely understood. We investigate the atomic mechanisms underlying both healthy regulation and dysregulation of the human protein tyrosine phosphatase SHP2, a key regulator of cellular signaling. While most pathogenic mutations cluster near the PTP/N-SH2 interface, the E139D and T42A mutations are located within the regulatory SH2 domains, an...

— Glaser, A., Padua, R., Ojoawo, A., Sullivan, C., Kern, D. 2025-12-14 00:00:00

AAV-delivered CRISPR-Cas9 elicits persistent retinal immune responses compared with transient responses to RNP

CRISPR-Cas9 is a powerful gene-editing tool with great potential for treating genetic diseases, including inherited retinal disorders. However, its bacterial origin can induce immune responses that may eliminate transduced cells, threatening editing efficiency. A deeper understanding of CRISPR-Cas9 immunogenicity is therefore needed. Previous studies have shown that systemic delivery via Cas9 induces an immune response, but the detailed inflammation and the impact of the vector remain unclear...

— Pulman, J., REN, D., Visticot, L., Malki, H., Yao, Y., De Cian, A., Ail, D., Concordet, J.-P., Dalkara, D., Fisson, S. 2025-12-14 00:00:00

In Situ Photoactivated Hydrogel Adhesive Dressings for Post Colon Polypectomies (PolypCures)

Colon polypectomy is a widely performed endoscopic procedure that reduces the incidence of colorectal cancer but leaves exposed colonic wounds susceptible to bleeding, perforation, and infection. The current standard of wound care, mechanical clips, is limited by technical complexity, high cost, and poor efficacy for large (> 2 cm in diameter) or difficult-to-access lesions. Here, we present PolypCure, an in situ photoactivated hydrogel adhesive dressing delivered via a single catheter, throu...

— Hu, X., Villarreal-Otalvaro, C., Liu, R., Hung, Y., Pratt, S. L., O'Toole, G., Berry, S., Jones, M., Rosenthal, A., Grinstaff, M. 2025-12-14 00:00:00

Microfluidic Immunocapture Device for Direct Detection of Lyme Disease

Lyme Disease is a multisystem infectious disease caused by the Borellia burgdorferi complex, and is a growing threat to public health. Approximately 476,000 people are infected with Lyme in the United States each year. Although Lyme is readily treated with antibiotics when detected early, early detection remains difficult. Current testing remains difficult because the standard 2-tiered ELISA/Western assay indirectly detects Lyme via measurement of a host immune response, which suffers from an...

— Wellmerling, K. M., Kirby, B. J. 2025-12-14 00:00:00

Molecular basis of noncanonical complement C3 activation by histamine

For fifty years the tick-over mechanism has been considered responsible for priming the activation of the complement system's alternative pathway through the reaction of a nucleophilic water molecule with C3 yielding C3(H2O), even though the exclusivity of this role has been challenged by the existence of extrinsic proteases that can cleave circulating C3 into C3b. Here we show that the biogenic amine histamine can activate C3 by reacting with the internal thioester bond yielding a novel spec...

— Fernandez, F. J., de la Paz-Garcia, K., Querol-Garcia, J., Ramos-Guzman, C. A., Martin-Merinero, H., Mares-Mejia, I., Alfonso-Gonzalez, L., Rodriguez de Cordoba, S., Tunon, I., Vega, M. C. 2025-12-14 00:00:00

In genomes we trust: assessing genomic reliability within the family Nectriaceae

The Nectriaceae includes major plant and human pathogens, yet the genomic foundation underpinning its taxonomy remains uneven and largely unassessed. We analysed 1,530 genome sequence assemblies to quantify metadata completeness, geographic and taxonomic bias, and assembly quality across the family. One-third of the assemblies lacked essential metadata, sequencing was heavily skewed toward a few agriculturally important lineages, and sampling of many genera was limited or nonexistent. BUSCO a...

— Villani, A., Ghionna, V., Susca, A., Menicucci, A., Prodi, A., Faino, L., Moretti, A., Baroncelli, R. 2025-12-14 00:00:00

AutoSTED: An automated workflow for STED super-resolution imaging of cell nuclei

The traditional microscopy workflow involves manual selection of objects one after the other. This is not only time consuming, but inevitably introduces human bias. Here, we describe a workflow, AutoSTED for identification of cell nuclei on wide-field fluorescence images and subsequent automated imaging of these nuclei at super-resolution by Stimulated Emission Depletion (STED) microscopy. We demonstrate that in an overnight run we are able to image hundreds of cells selected without bias. Th...

— Leger, D., Ivanisevic, M., Lenart, P. 2025-12-14 00:00:00

Dpp and Immune Response Pathways Factors Mediate Paracrine Induction of Senescent Cells in Drosophila

Transition toward senescence is a cellular response to different stressors like ionizing radiation, telomere shortening or oncogene activation. This phenomenon is evolutionarily conserved across species, from insects to humans. Senescent cells (SCs) permanently withdraw from the cell cycle and undergo a series of physiological changes, most notably the acquisition of a robust secretory activity characterized by the release of numerous molecules, including cytokines, chemokines, and metallopro...

— Garcia-Arias, J. M., Ruiz-Losada, M., Azpiazu, N., Morata, G. 2025-12-14 00:00:00

IDR-dependent MORC1 bodies limit chromatin accessibility to tune transposon repression

Germline-specific MORC1-mediated transposon repression intersects with the MIWI2-piRNA pathway and involves H3K9me3 deposition, yet the underlying mechanism remains unclear. Here, we show that MORC1 assembles nuclear bodies in gonocytes. Using a doxycycline-inducible MORC1 expression system in NIH3T3 cells, we find that condensate formation is confined to the nucleus via an IDR containing a bipartite NLS, and that TRIM28, a corepressor that recruits the H3K9 methyltransferase SETDB1, is enric...

— Isota, Y., Li, P., Sakata, K., Chiwata, H., Kosako, H., Yamanaka, S., Yamazaki, H., Siomi, M. C. 2025-12-14 00:00:00

Ribosomal Epistatic Interactions Drive the Emergence of High-Level Streptomycin Resistance in Escherichia coli

The widespread use of antibiotics has raised serious concerns about the emergence and dissemination of antibiotic resistance in the environment. Studies reveal that environmental exposures to antibiotics and other non-antibiotic pollutants can promote the development of high-level antibiotic resistance via de novo mutations. However, specific genotypes conferring strong resistance in resistant mutants, particularly the roles of co-occurring mutations, remained poorly understood. This study fi...

— Xu, F., Xing, Y., Men, Y. 2025-12-14 00:00:00

Environment and physiology shape antiphage system expression

Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of antiphage systems expression patterns is lacking. Here, we combine publicly available RNA-seq data from 14 different species with an original RNA-seq dataset of 15 Escherichia coli strains across six environmental conditions and two growth stages. Using this data, we explore the transcription pattern...

— Paoli, L., Laruelle, B., Lavenir, R., Loubat, A., Tesson, F., Gaborieau, B., Bernheim, A. 2025-12-14 00:00:00

Are frameworks independent from CDRs in antibodies? Exploring CDR-framework correlation networks of antibodies

The growing success of monoclonal antibodies (mAbs) in therapies highlights the importance of the humanization process in antibody design. This key step involves grafting selected complementarity-determining regions (CDRs) onto human frameworks (FWs) to reduce immunogenicity. However, the effect of this process on the antibody's structure and dynamics is underexplored. This study uses molecular dynamics simulations to evaluate whether different CDRs can impact the framework of the antibody. P...

— Leal, A. D., Lopes de Oliveira, P. S., Bortot, L. O. 2025-12-14 00:00:00

PD-L2 Regulates Natural Antibody and IL-10 Secretion by B-1 cells

B-1 cells are innate-like lymphocytes that play a critical role in homeostasis by secreting natural antibodies, typically IgM, and immunosuppressive molecules such as IL-10. However, the regulation of these processes in B-1 cells remains poorly understood. Here, we demonstrate that PD-L2, a surface receptor expressed by all B-1 cells, regulates B-1 cell effector functions. We show that in contrast to the Mus musculus castaneus mouse and other mammals, commonly used laboratory mouse strains ha...

— Amendt, T., Vanes, L., Tybulewicz, V. 2025-12-14 00:00:00

Rigorous Quantitative Analysis of Nonlinear Uncertain Biomolecular Systems using Validated Methods

The paper addresses the critical challenge of accurately characterising steady states in biomolecular systems, which are often complex, nonlinear, multistable and subject to significant uncertainties. Traditional numerical methods often fail to provide complete or guaranteed solutions under these conditions. To overcome these limitations, the research proposes and evaluates the application of interval analysis methodologies. We provided algorithms for interval Newton and interval Krawczyk met...

— PRAKASH, R., Sen, S. 2025-12-14 00:00:00

Detection of Mid-parent Heterosis Genes in Large-Scale Unreplicated RNA-Seq Experiments

Mid-parent heterosis (MPH), characterized by hybrid trait values deviating from the mid-parent average, is a well-documented phenomenon whose genetic basis remains poorly understood. Identifying genes associated with MPH is crucial for uncovering the molecular mechanisms underlying heterosis. Recent large-scale RNA-sequencing (RNA-seq) experiments enable the evaluation of heterosis genes across numerous families; however, replication is often infeasible due to cost and labor constraints, resu...

— Qi, Y., Liu, P. 2025-12-14 00:00:00