Browse Articles

Dissecting the propensity of RIM1 subdomains to form phase condensates

Abstract Emerging evidence indicates that liquid-liquid phase separation (LLPS) may orchestrate synaptic vesicle and active zone (AZ) protein organization in presynaptic terminals via biomolecular condensates. A protein’s LLPS propensity is determined by intrinsic factors such as structural disorder, amino acid composition, multivalent interactions, and regulation by post-translational modifications, highlighting the need for a systematic dissection of condensate-forming regions in a cellular context. Here, we systematically examined the condensation properties of the AZ protein RIM1 using an established cell-based overexpression assay and found that, while full-length RIM1 exhibits the highest condensation propensity in our assay, even fragments as short as ~ 250 amino acids form condensate-like assemblies in HEK cells. For all but four fragments, their propensity to be enriched in droplets over the intracellular solution quantitatively correlates with their length. We identified a minimal region that closely reproduces key full-length RIM1 droplet properties with regard to abundance per cell and volume, comprising the zinc finger domain, the intrinsically disordered region 1 (IDR1), the proline-rich motif 1 (PRM1), the PDZ- and C2A-domains, and two non-condensing regions, the sequences containing either PRM2 and IDR2 or PRM1 till the end of the C2A-domain. In contrast to in vitro data, RIM-BP2 promotes phase condensation of full-length RIM1 only at lower RIM1 expression levels and differentially impacts the phase condensation capacity of different RIM1 truncation mutants. Taken together, our results define the phase condensation behavior of different RIM1 sequence elements and show that enrichment of the protein in the phase condensates increases exponentially with the length of the fragments.

Antibiotic-induced Malassezia expansion in the infant gut promotes early-life immune dysregulation and airway inflammation in mice

A teleost-specific oxygen–immunity axis where FIH activates NF-κB via competitive IκBα binding

Global warming–induced aquatic deoxygenation poses a severe physiological challenge to teleosts, often influencing their immune defense mechanisms. While aquatic organisms are under evolutionary pressure to balance metabolic adaptation with pathogen resistance, the molecular strategies they employ to overcome high pathogen loads under hypoxic stress remain poorly understood. Here, an oxygen–immunity regulatory axis was identified in teleosts, in which the oxygen sensor FIH (factor inhibiting HIF) activated the NF-κB pathway by competitively displacing p65 from IκBα. Experiments with FIH mutants showed that NF-κB activation did not require FIH hydroxylase activity. In vitro, FIH bound IκBα, promoted p65 nuclear translocation, and increased inflammatory gene expression. FIH knockdown blunted these responses. In vivo, CRISPR/Cas9-generated drfih –/– zebrafish showed reduced NF-κB-driven inflammation, altered responses to LPS challenge, and a dose-dependent trade-off in Vibrio anguillarum infection, with reduced resistance at a low dose but mitigated immunopathology at a high dose. AlphaFold3 modeling and mutational analyses pinpointed a competitive interface. In human cells, FIH–IκBα binding occurred without NF-κB activation. Notably, replacing a C-terminal segment of human IκBα with the teleost counterpart restored FIH-dependent competition and NF-κB activation, indicating lineage-specific structural divergence. Extensive cross-species predictions revealed that several aquatic vertebrates, an amphibian, and a shrimp species possessed a competitive interface, whereas the terrestrial species examined did not. These findings revealed a hydroxylase-independent mechanism, likely associated with aquatic lineages, that linked oxygen sensing to innate immunity and had implications for vertebrate evolution, climate-driven hypoxia, and aquaculture health.

Optimization of direct organogenesis from immature inflorescence explants of coconut (Cocos nucifera L.)

Biophysical modeling for accurate T cell specificity prediction of viral and tumor antigens

State-switching navigation strategies in <i>Caenorhabditis elegans</i> are beneficial for chemotaxis

Animals employ different strategies for relating sensory input and behavioral output to navigate sensory environments, but what strategy to use, when to switch and why remain unclear. Caenorhabditis elegans navigate by combining “steering” (small heading changes) with “turn” (large reorientations). It is unknown whether transitions between these elements are driven solely by sensory input or also by persistent internal states. It is also unclear how worms sometimes appear to exit turns such that they are already oriented toward a goal, despite their presumed lack of spatial awareness during turns. We address these questions with measurements of sensory-guided navigation and a statistical model of state-dependent control. Worm navigation is well described by a sensory-driven, two-state-switching model whose states persist for seconds and produce distinct sensorimotor mixtures: one state is steer-enriched, the other turn-enriched. This hierarchical temporal organization challenges the view that gradient-climbing strategies are static and purely stimulus-locked. Instead, sensory input causally modulates transitions between persistent states, creating the appearance of “directed turns” when exiting the turn-enriched state. Measurements using genetically perturbed animals and modeling with data-constrained reinforcement-learning both show that state switching enhances gradient-climbing performance. Together, measurement, perturbation, and modeling reveal that state switching is functionally beneficial, organizing behavior across time—a principle that may generalize across species and contexts.

CRISPR-Cas9-mediated knock-in of cytomegalovirus US2 provides an alternative strategy for generating hypoimmunogenic hiPSC lines

Dual Photoredox/Cobalt Catalysis Enabled Regiospecific Markovnikov Hydroboration of Unactivated Mono-, Di-, and Trisubstituted Alkenes

Dual-chirality flexagon linkages with infinite eversion and surface reconfigurability

The flexagon, a classical kirigami structure capable of revealing hidden faces through eversion, has long captivated researchers. However, its potential for robust engineering applications has been limited by inherent structural discontinuities and unclear kinematic mechanisms. Here, we introduce a cyclic graph model and an idealized dual-chirality flexagon linkage with infinite eversion to explain the underlying mechanics of this eversion. We demonstrate that the eversion exhibits topological periodicity and multiple symmetries, while its kinematics correspond to a cyclic permutation of congruent axis sets induced by bifurcated motion. By tuning topological parameters, we construct a comprehensive atlas of the flexagon family. To address challenges in physical implementation, we propose a linkage convertibility strategy that eliminates mechanical interference and enables the design of reconfigurable, deployable networked structures. Furthermore, we develop an interchangeable-chirality flexagon that achieves an exponential expansion in accessible surface states, where the incremental states added in each expansion follow a geometric progression, p ( p − 1 ) g (where p denotes the eversion period and g represents the recursive generation index). This work bridges the gap between abstract topological concepts and physical realizations, offering a pathway to transform classical kirigami into advanced engineering linkages. It also provides foundational insights for related eversion systems, including Möbius strips, kaleidocycles, and other cyclic topological structures.

Effects of incremental mandibular advancement on upper airways morphology and anatomical structures: a preliminary CT scan study on body donors

A 1970s patent that changed the course of commercial biotechnology

Motor cortex directly excites the substantia nigra pars reticulata, the basal ganglia output nucleus

Abstract Inhibitory neurons of the substantia nigra pars reticulata (SNr) serve as a primary output through which the basal ganglia regulate behavior. Using a virally targeted optogenetic approach, combined with whole cell patch-clamp recordings of SNr neurons, we show that, in mice, projection neurons of both primary and secondary motor cortices (M1 and M2) form monosynaptic excitatory connections onto different subpopulations of GABAergic SNr neurons. Furthermore, photostimulation of these cortical axon terminals markedly increases SNr neuron firing rate. To investigate the spatial organization of cortical input to the SNr, we employed a transsynaptic viral-labelling approach to identify SNr neurons receiving monosynaptic input from either M1 or M2. We found a topographical organization of the M1 and M2 projections in SNr. Chemogenetic inhibition of M1- and M2-targeted SNr neurons induced opposing changes in spontaneous behavior. These findings reveal functional pathways by which the motor cortex can directly modulate basal ganglia output to downstream targets.

Dynamic monitoring of antibody drug conjugates targeting TROP2 or HER2 in breast cancer using circulating tumor cells

Antibody–drug conjugates (ADCs) target surface proteins on cancer cells, leading to internalization and delivery of a drug payload, thereby enhancing selectivity and minimizing toxicity. ADCs against TROP2 (Sacituzumab govitecan) or HER2 (T-DXd) have demonstrated efficacy in metastatic breast cancer, yet paradoxically, outside of HER2 -amplified breast cancers, expression levels of these breast cancer-enriched epitopes in tumor biopsies have not been strongly correlated with clinical response. We undertook serial quantitative imaging of circulating tumor cells (CTCs) in a prospective cohort of 35 patients treated with either of these ADCs. At the single-cell level, expression of TROP2 and HER2 within individual patients is highly heterogeneous in both CTCs and paired tumor biopsies. Measurement of these epitopes on CTCs immediately prior to ADC therapy does not predict depth of clinical response. However, absence of CTCs or &gt;80% reduction in CTC numbers after three weeks of treatment (CTC Low ) predicts durable response, compared with CTC High cases (TROP2: HR 5.15, P = 0.012; HER2: HR 6.01, P &lt; 0.001). Targeted epitopes are not commonly downregulated on CTCs at the time of acquired clinical resistance, and switching between TROP2- and HER2-targeting ADCs sharing similar payloads infrequently leads to second-line response. Thus, while CTC burden is correlated with response to these ADCs, the level of TROP2 or HER2 expression is poorly predictive. These findings point to sensitivity to the drug payload as a potential driver of clinical response to currently approved ADCs in breast cancer.

Nematicidal potential of Carissa carandas seed extract against Meloidogyne incognita and identification of its bioactive compounds

Mutant KRAS peptide vaccine with dual checkpoint blockade in metastatic colorectal cancer: a phase I trial

A genome-wide CRISPR screen reveals how diatoms thrive in dynamic light

Diatoms are a highly diverse algal group with outsized impact on global primary production and marine carbon sequestration. They are red lineage phototrophs of complex endosymbiotic origin and therefore evolutionarily divergent from plants and other green lineage phototrophs that typically serve as photosynthesis models. To accelerate the discovery of unique diatom biology, we developed a genome-wide CRISPR/Cas9 screen in the marine diatom, Phaeodactylum tricornutum. Dynamic light conditions are common in nutrient-rich, well-mixed marine environments in which diatoms thrive. The P. tricornutum mutant library was grown in different light regimes, including both high light and fluctuating light. We identified a broad set of genes required for survival specifically in dynamic light, including effectors of cyclic electron flow (CEF) and enzymes catalyzing posttranslational modifications of Calvin cycle enzymes. Among genes of unknown function identified, we demonstrated that the red lineage-exclusive gene STROBE1 is a CEF potentiator required for CEF-dependent generation of a trans-thylakoid proton gradient. STROBE1 and other genes identified in this screen reveal unexpected mechanisms underlying the adaptation of diatoms to dynamic light environments. This genome-wide genetic screen in P. tricornutum will accelerate the unbiased discovery of novel gene functions in these ecologically important organisms.

Genetic interference of distinctive Mycobacterium tuberculosis peptidoglycan modifications enhances β-lactam susceptibility and reveals expression-sensitive host immune dynamics

Abstract The high mortality associated with tuberculosis (TB), alongside the lack of efficient therapeutics against emerging multidrug-resistant Mycobacterium tuberculosis ( Mtb ) strains, emphasizes the need for novel antitubercular targets. Mycobacterial peptidoglycan (PG), displaying characteristic modifications comprising the amidation of D- iso -glutamate (D- i Glu) and the N -glycolylation of muramic acid, is therefore a promising therapeutic target. The genes encoding the enzymes mediating these modifications ( murT / gatD and namH ) were silenced in Mtb using CRISPR interference (CRISPRi) to investigate their impact on β-lactam susceptibility and host immune responses. First, qRT-PCR confirmed successful target mRNA knockdown and phenotyping assays corroborated the essentiality of D- i Glu amidation for mycobacterial growth, in contrast to muramic acid N -glycolylation. The susceptibility assays demonstrated that both PG modifications promote β-lactam resistance. Indeed, we observed reductions in the minimum fractional inhibitory concentration index (FICI min ) value for AMX/MEM + CLA and EMB combinations following the depletion of both PG modifications. Furthermore, D- i Glu amidation was found to promote Mtb fitness within THP-1-derived macrophages 6 days post-infection. Infection with MurT/GatD-depleted Mtb was associated with increased IL-1β and decreased IL-10, whereas NamH depletion was linked to increased IL-1β and IL-10 levels. Altogether, our findings unveiled the potential of targeting these PG modifications for the development of innovative therapeutic regimens against TB.

Author Correction: Droughts preceding tree mortality events have increased in duration and intensity, especially in dry biomes

Direct demonstration of electric chirality control in a helimagnetic YMn ₆ Sn ₆ by spin-polarized neutron scattering

The spiral handedness of magnetic moments, referred to as chirality, gives rise to emergent electromagnetic phenomena in helimagnets. In insulating helimagnets, known as multiferroics, the cycloidal spin structure induces electric polarization by utilizing the inverse Dzyaloshinskii–Moriya mechanism. Spin-polarized neutron diffraction experiments, which directly probe circular spin arrangements, clearly demonstrated that an electric field controlled the chirality in multiferroic helimagnets. On the other hand, it was unclear until recently how the chirality could be controlled in metallic helimagnets where a large electric field cannot be applied, while the chirality control technique in metallic helimagnets should enable the exploration of chirality-dependent spintronic functionalities. Recently, Jiang et al. succeeded in controlling the chirality of a spiral structure by the simultaneous application of a magnetic field and electric current in a metallic helimagnet, utilizing the nonreciprocal electronic transport as an indirect probe of chirality, highlighting the need for a neutron diffraction experiment that directly probes the chirality. Here, we directly demonstrate the chirality control in a metallic helimagnet YMn 6 Sn 6 by means of spin-polarized neutron diffraction, which should give rise to a firm basis for the development of future helimagnetic spintronics.

Network analysis of anxiety and depression in college students with different levels of physical activity