Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Host EV derived lipids promote malaria parasite development via mosquito fatty acid oxidation

Malaria parasites must transition between mammals and mosquitoes, but how they adapt to such distinct environments is unclear. We show that blood from infected mammals buffers this environmental shift by packaging parasite-induced signals into extracellular vesicles (EVs). EVs internalized by mosquito midgut increases expression of VLCAD and raises levels of a 22-carbon fatty acid, driving fatty acid breakdown and acetyl-CoA production. The parasite exploits this metabolic shift to synthesize its own lipids during oocyst growth. Stable isotope tracing confirmed that13C4-labelled behenic acid is degraded and incorporated into parasite fatty acids. Lipidomic profiling further revealed that ceramides enriched in the EVs are key mediators. These findings identify a mechanism by which host bood-derived EVs reprogram mosquito lipid metabolism to promote parasite transmission.

microbiology↗

bioRxiv2025

Immunometabolic determinants of long-term response in leukemia patients receiving CD19 CAR T cell therapy

Although most patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) receiving CD19-targeted chimeric antigen receptor (CAR) T cell therapy achieve remission, loss of CAR T cell functionality and subsequent relapse remains an unmet therapeutic need. We applied an integrative approach to study the immunometabolism of pre- and post-infusion CD19-CAR T cells of patients with relapsed/refractory B-ALL. Pre-infusion CAR T cells of long-term responders (LTR) had increased oxidative phosphorylation, fatty acid oxidation, and pentose phosphate pathway activities, higher mitochondrial mass, tighter cristae, and lower mTOR expression compared to products of short-term responders. Post-infusion CAR T cells in bone marrow (BM) of LTR had high immunometabolic plasticity and mTOR-pS6 expression supported by the BM microenvironment. Transient inhibition of mTOR during manufacture induced metabolic reprogramming and enhanced anti-tumor activity of CAR T cells. Our findings provide insight into immunometabolic determinants of long-term response and suggest a therapeutic strategy to improve long-term remission.

immunology↗

bioRxiv2025

Lattice Instability Drives Formation of Protofilament Clusters at the Microtubule Plus End Tips

Microtubules (MTs) are dynamic cytoskeletal filaments composed of - and {beta}-tubulin protein dimers. They are crucial for maintaining cell structure, facilitating intracellular transport, and ensuring proper chromosome segregation among other things. These biological functions are influenced by the dynamic instability of the MT plus-end tip. Recent simulations have discovered formation of protofilament (PF) clusters at the MT plus-end tip, but reliable extrapolation of PF cluster dynamics and detailed microscopic mechanism are yet to be developed to understand their behavior thoroughly. In this work, we have constructed, from "bottom up", a relatively high resolution coarse-grained (CG) molecular dynamics (MD) model for tubulins with 20 CG sites per tubulin monomer, performed extensive CG MD simulations on MT lattices with 8 and 40 layers of heterodimers, and conducted comprehensive atomistic-level analysis. Our findings demonstrate that, in both GTP and GDP states, PF clusters are stable up to tens of microseconds of CG MD simulation time during spontaneous outward bending relaxation. PF clustering is initiated by longitudinal relaxation, stabilized by residual lateral interaction in the PF clusters. This process is thermodynamically driven by intrinsic lattice instability. In longer microtubules, this instability accumulates and further facilitates PF bending and clustering at the plus-end tip, but it can also be released via lattice curvature and supertwist. GDP-MTs form more PF clusters than GTP-MT on average and undergo more lateral cleavage and faster bending relaxation due to weaker lateral interactions, which facilitates MT catastrophe. GTP-MT forms flatter and more rigid PF clusters that favor nucleotide addition. Our findings highlight the critical role of lattice instability in microtubule dynamics and offer new insights on the conformational variability of MT plus-end tips. SIGNIFICANCEThe dynamical structure and behavior of microtubule (MT) plus-end tips remains an important topic in structural and computational biophysics. For the recently discovered protofilament clusters at MT plus-end tips, this study provides a mechanism for their formation through comprehensive analyses of tubulin-tubulin interaction interfaces in all-atom simulations of complete MT lattices. This study also makes long-time predictions for the dynamics of PF clusters through a coarse-grained model for the tubulin heterodimers to extend the effective simulation time and system size, while preserving key details of the lateral and longitudinal interaction interfaces. The findings deepen understanding of the life cycle of PF clusters, while adding new insight on microtubule dynamics and the role of lattice destabilization.

biophysics↗

bioRxiv2025

Dynamic BH3 profiling predicts clinical outcomes in acute myeloid leukemia

Predictive biomarkers can potentially meet the need for improved drug assignment in acute myeloid leukemia (AML). Fewer than half of AML patients have actionable mutations: consequently, targeted therapy achieves remission in only a fraction of those who have them. Dynamic BH3 Profiling (DBP), a functional assay, can measure changes in ex vivo drug-induced apoptotic priming in multiple cancers. To assess the feasibility and predictive capacity of DBP in AML, we prospectively tested DBP using a fixed-drug panel in myeloblasts from 92 patients. We generated a database combining genetic and functional annotation. Established AML clinical and genetic prognostic characteristics were associated with drug-induced apoptotic priming. We observed distinct interpatient sensitivities to single drugs or combinations with the BCL2-inhibitor venetoclax, and intrapatient apoptotic priming differences based on CD123-expression within distinct cell subpopulations. DBP further predicted the likelihood of remission to chemotherapy and targeted agents, supporting its use to identify optimal personalized therapy. Statement of significanceDynamic BH3 profiling provides patient-specific drug vulnerability data in real-time to inform prognosis and therapy selection. Key takeawaysO_LIDynamic BH3 profiling can be performed on bone marrow and leukemic blood from AML patients in 48 hours. C_LIO_LIKnown clinical prognostic factors associate with drug-induced apoptotic priming in AML. C_LIO_LIDrug-induced apoptotic priming identifies drug vulnerabilities in individual patients and predicts clinical response to chemotherapy and small molecule inhibitors. C_LI

cancer biology↗

bioRxiv2025

Durability of DNA-LNP and mRNA-LNP Vaccine-Induced Immunity Against SARS-CoV-2 XBB.1.5

mRNA-lipid nanoparticle (LNP) vaccines induce robust adaptive immune responses and have proven highly effective against SARS-CoV-2. However, their long-term effectiveness is limited by waning humoral responses, which decline substantially within the first six months post-boost vaccination. DNA-LNPs are being investigated as an alternative vaccine platform, offering prolonged antigen expression and robust immunity. Here, we present the first comparison of SARS-CoV-2 DNA- and mRNA-LNP vaccines in a long-term in vivo challenge model. Both nucleic acid platforms induced strong neutralizing antibody responses and conferred equivalent protection in Syrian hamsters challenged three weeks post-boost. Notably, DNA-LNP vaccination maintained high binding and neutralizing antibody titers six months post-boost, whereas mRNA-LNPs exhibited a marked decline. Correspondingly, while DNA-LNPs completely protected from weight loss, viral replication, and lung pathology at this late timepoint, mRNA-LNP vaccination conferred minimal protection. These findings demonstrate that DNA-LNPs can sustain durable immunity, highlighting their potential as a next-generation vaccine platform that could reduce the need for frequent boosters.

immunology↗

bioRxiv2025

Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing

Background and objectivesVisible-light optical coherence tomography (vis-OCT) has enabled the visualization of retinal structures and functions beyond the capabilities of conventional OCTs. However, to reconstruct high-quality images, vis-OCT requires special post-processing, including balanced detection. An open-source, standardized vis-OCT data processing software is essential for clinical applications and translation of vis-OCT. MethodsWe developed Vis-OCT Explorer, an open-source, modular Python-based software for processing vis-OCT images. In addition to the standard spectral-domain OCT processing pipeline - including k-space resampling, dispersion compensation, and fast Fourier transformation - Vis-OCT Explorer offers unique dual-spectrometer balanced detection, short-time-Fourier transformation (STFT) based dispersion compensation coefficient optimization, and GPU-accelerated processing. We evaluated the reconstruction performance by quantifying a quality index extracted from individual B-scan images. We also assessed the repeatability of retinal thickness measurements by five operators on images acquired from different testing sites using the intraclass correlation coefficient (ICC) analysis. ResultsBalanced detection and STFT-based dispersion compensation significantly increased the quality index of reconstructed B-scan images. ICC values of the retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements from four testing sites exceeded 0.8 in 87.5% of the macular-centered images. The ICC of RNFL thickness measurements on all optic nerve head-centered images is above 0.8, showing strong repeatability across users. ConclusionsVis-OCT Explorer provides high-quality image processing and enables highly repeatable measurements on vis-OCT human retinal images. It facilitates future multicenter clinical tests to validate vis-OCTs clinical efficacy.

bioengineering↗

bioRxiv2025

Common Phenomenal and Neural Substrate Geometry in Visual Motion Perception.

What is a possible physical substrate of the qualitative aspects of consciousness (qualia)? Answering this question is a central goal of consciousness research. Due to their subjective and ineffable nature, finding a quantitative way to characterise qualia from verbal description has thus far proven elusive. To overcome the challenge of expressing subjective experience, recent structural and relational approaches have been proposed from mathematics. Yet, as far as we know, no attempts have been made to evaluate the relationship between a certain structure of qualia and the structure of a candidate underlying physical substrate. Towards this ambitious goal of linking the structures of qualia and physical, we set out to make an empirical first step by focusing on experienced dissimilarity of visual motion in human participants and stimulus-evoked neural population response geometry recorded from mouse primary visual cortex. From human participants (N=171), we obtained dissimilarity ratings of visual motion experiences induced by 48 stimuli, spanning across 8 directions and 6 spatial frequencies. Analysis revealed a human dissimilarity structure that was not well captured by a simple monotonic function of physical motion-direction difference alone nor by a pure orientation-symmetry account. From nine individual mice, we recorded single-neuron activity (n=751) with optical imaging in both awake and lightly anaesthetised conditions (isoflurane 0.6-0.8%). From neuron population responses to a similar set of motion stimuli, we computed a distance matrix that is comparable to our human dissimilarity matrix. Quantitative analyses show structural commonalities between a human dissimilarity structure and mouse neural structure, where a categorical organisation of stimulus direction best explained both. These commonalities were similar in awake and anaesthetised recordings, suggesting that this coarse V1 geometry is relatively insensitive to this type of anaesthesia; future work combining behaviour with causal intervention is required to relate such neural structures to conscious experience. Finally, we list several empirical factors that can be improved to promote our qualia structure approach in the future. Graphical AbstractSimilarity structures derived from a pairwise similarity rating task in humans revealed a mismatch between physical stimuli and subjective experience of similarity of visual motion: participants robustly rated their experience of opposite direction stimuli as similar. In mice, we used 2-photon Ca2+ imaging to record the activity of c.80 neurons per mouse in the primary visual cortex (V1) of nine mice. By computing a correlation matrix that records the similarity of responses to the same pairwise comparisons as in humans across all neurons, we can then represent neuronal distance. This revealed that mice neurons also exhibited the same dissociation between physical stimuli and responses as in humans at lower spatial frequencies. By comparing these dissimilarity and distance matrices using linear mixed effects modelling, we showed that a categorical model, not direction or orientation, best explains both human and mice data. Ultimately, this study is a methodological proof-of-concept for comparing structures of experience to candidate structures of a possible neural substrate in order to constrain their candidacy. O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/679834v2_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@768e3forg.highwire.dtl.DTLVardef@174e501org.highwire.dtl.DTLVardef@166cf75org.highwire.dtl.DTLVardef@be1a6e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVisual motion feels more similar for opposite than diagonal directions C_LIO_LIPairwise similarity ratings reveal structure of visual motion experience C_LIO_LIHuman motion experience and mouse visual cortex share a common geometry C_LIO_LIMouse visual cortex codes motion similarly when awake and lightly anaesthetised C_LI

neuroscience↗

bioRxiv2025

Correcting Non-Uniform Milling in FIB-SEM Images with Unsupervised Cross-Plane Image-to-Image Translation

MotivationFocused Ion Beam Scanning Electron Microscopy (FIB-SEM) is an advanced Volume Electron Microscopy technology with growing applications, featuring thinner sectioning compared to other Volume Electron Microscopes. Such axial resolution is crucial for accurate segmentation and reconstruction of fine structures in biological tissues. However, in reality, the milling thickness is not always uniform across the sample surface, resulting in the axial plane looking distorted. Existing image processing approaches often: (i) assume constant section thickness; (ii) consist of multiple separate processing steps (i.e., not in an end-to-end fashion); (iii) require ground truth images for modeling, which may entail significant labor and be unsuitable for rapid analysis. ResultsWe develop a deep learning method to correct non-uniform milling artifacts observed in FIB-SEM images. The proposed method is an image-to-image translation technique that can mitigate image distortions in an unsupervised manner. It conducts cross-plane learning within 3D image volumes without any ground truth annotations. We demonstrate the efficacy of our method on a real-world micro-wasp dataset, showcasing significantly improved image quality after correction with qualitative and quantitative analysis. Contactpfister@seas.harvard.edu, jingpengw@lglab.ac.cn

bioinformatics↗

bioRxiv2025

In vitro evaluation of protein-protein interactions in the rice KAI2 ligand signaling complex

KARRIKIN INSENSITIVE 2 (KAI2)/DWARF14-LIKE (D14L) plays key roles in land plant development, environmental responses, and the establishment of arbuscular mycorrhizal symbiosis, likely acting as the receptor for unidentified signaling molecules termed KAI2 ligands (KLs). KL perception by KAI2/D14L promotes DWARF3 (D3)/MORE AXILLARY GROWTH2 (MAX2) F-box protein-mediated ubiquitination of SUPPRESSOR OF MAX2 1 (SMAX1) proteins, thereby transducing the KL signals. Although genetic and in vivo assays have demonstrated the functions of these components, the biochemical details of their interactions remain elusive. Here we investigated physical interactions between rice D14L, D3, and OsSMAX1 in vitro using desmethyl germinone (dMGer), a recently developed KL analog. dMGer elicited KL responses in rice with higher activity and pathway specificity than a widely used KL analog (-)-GR24. dMGer, but not (-)-GR24, directly bound to D14L and promoted the interaction between D14L and D3 in vitro. The interaction between D14L and OsSMAX1 was also enhanced by dMGer. Furthermore, we identified the domain of OsSMAX1 that distinguishes it from its paralog DWARF53 (D53), which is associated with the strigolactone signaling complex. These findings propose a model of the interactions among KL signaling components and highlight the role of the ligand in the signaling complex.

plant biology↗

bioRxiv2025

Anesthesia Induces Shifts in Spatial Frequency Preference in the Primary Visual Cortex

This study examined the impact of general anesthesia on visual processing in the mouse primary visual cortex (V1). By directly comparing visual responses in the same layer 2/3 neurons between the awake and anesthetized states, we found that isoflurane anesthesia significantly shifts the preferred spatial frequency (SF) of neurons to lower values while leaving orientation tuning intact. This downward SF shift impaired the ability to encode fine visual details (high-SF) but not coarse information (low-SF). The shift was observed across all recorded cell types--including excitatory, somatostatin-expressing (SOM), and parvalbumin-expressing (PV) inhibitory neurons--though their respective magnitudes and underlying patterns were distinct. Furthermore, modulation of response gain and tuning sharpness was observed exclusively in SOM neurons. These results highlight the specific effects of anesthesia, which vary with visual feature and neuron type. These findings suggest that reduced sensory perception during anesthesia is linked to a degradation in spatial resolution at the cellular level.

neuroscience↗

bioRxiv2025

Aphid-derived cross-kingdom RNA dynamics underpin maize resistance

Aphids are major pests of maize (Zea mays), yet the molecular mechanisms underlying their interactions with host plants remain poorly understood. Here, we identified and functionally characterized long non-coding RNAs (lncRNAs) from the aphid-specific Ya gene family in the cereal-specialist aphids Rhopalosiphum maidis and R. padi. We showed that Ya genes formed lineage-specific clusters and were transcriptionally active across both species. Multiple Ya transcripts secreted into maize tissues exhibited remarkable stability compared with rapidly degraded aphid mRNAs and migrated systemically, as visualized in planta using an RNA switch-controlled RNA-triggered fluorescence system. RNA interference of Ya genes significantly reduced aphid fecundity, while ectopic expression of Ya lncRNAs in maize enhanced aphid colonization. Importantly, maize genotypes differing in aphid resistance selectively influenced the persistence of aphid mRNAs but not Ya lncRNAs, indicating a decoupled fate of distinct aphid RNA classes in planta. These findings establish Ya lncRNAs as cross-kingdom effectors critical for aphid virulence, and suggest new molecular markers for breeding aphid-resistant maize.

plant biology↗

bioRxiv2025

RIP3 and MLKL regulate Hepatic ER stress in alcohol-associated liver disease and pharmacological ER stress models: insights beyond necroptosis

Background and AimEndoplasmic reticulum (ER) stress is an important contributor to liver disease progression, including alcohol-associated liver disease (ALD). While receptor-interacting protein kinase-3 (RIP3) and mixed lineage kinase domain-like pseudokinase (MLKL) are known for their roles in necroptosis, emerging evidence highlights their non-canonical functions in metabolic regulation and cellular stress responses. However, their specific role in regulating hepatic ER stress remains unclear. This study investigates how RIP3, its kinase activity, and MLKL regulate ER stress pathways during chronic ethanol exposure and pharmacological ER stress induction. MethodsRip3-/-, Rip3K51A/K51A and Mlkl-/- mice alongside WT controls and pharmacological necroptosis inhibitors were used to study the role of RIP3 and MLKL in modulating ER stress. Chronic ethanol feeding and pharmacological agents (tunicamycin, thapsigargin) were utilized to induce ER stress in vivo and in isolated primary hepatocytes. ER stress markers were assessed by qPCR and western blot, ER expansion was evaluated by confocal microscopy, and hepatocyte viability was measured using MTS assay. ResultsChronic ethanol increased expression of ER stress markers in WT mice; this response was attenuated in Rip3-/- mice. Tunicamycin exposure increased hepatic ER stress markers in WT mice; this response was diminished in Rip3-/-, Rip3K51A/K51A and Mlkl-/-mice. In primary hepatocytes, genetic and pharmacological inhibition of RIP3 and MLKL also reduced thapsigargin-induced ER stress responses. Hepatocytes isolated from Rip3-/-, Rip3K51A/K51Aand Mlkl-/- mice exhibited enhanced cell viability under ER stress conditions compared to hepatocytes from WT mice, which was associated with ER expansion as a potential mechanism for mitigating ER stress. ConclusionThis study highlights a novel function of RIP3 and MLKL in regulating hepatic ER stress responses, expanding their known roles beyond programmed necrosis. Impact and ImplicationsThis study provides new mechanistic insight into how RIP3 and MLKL regulate hepatic ER stress responses, extending their roles beyond necroptosis. By demonstrating that genetic or pharmacological inhibition of Rip3, RIP3 kinase activity and Mlkl attenuates ER stress signaling, reduces cell death, and promotes adaptive ER remodeling, our findings identify these proteins as key modulators of hepatocyte survival under stress. These results are important for researchers and clinicians focused on alcohol-associated liver disease and other ER stress-driven liver disorders, as they highlight novel therapeutic targets. In practical terms, modulation of the RIP3- MLKL axis could inform the development of interventions aimed at enhancing ER stress resilience, with potential applications in drug development for ER stress-associated liver injury.

cell biology↗

bioRxiv2025

Phytoplankton community structure and photophysiological strategies in the oligotrophic Indian Ocean spawning ground of Southern Bluefin Tuna

The Argo Basin, a persistently oligotrophic seascape downstream of the Indonesian Throughflow (ITF), is the only known spawning ground of Southern Bluefin Tuna (Thunnus maccoyii). Its surface waters are capped by the warm, low saline, nitrate-depleted Pacific Ocean outflow, that leads to intense water-column stratification and chronic nutrient scarcity. During the BLOOFINZ campaign (R/V Roger Revelle, January-March 2022), we combined high-resolution underway surveys with Lagrangian experiments to examine hydrography, nutrient stoichiometry, and phytoplankton photophysiology across the basin. This study was motivated by the need to: 1) identify the phytoplankton communities capable of persisting in this nutrient-impoverished region, and 2) uncover the unique photophysiological traits that underpin their survival and growth, particularly under acute nitrate limitation. Nutrient fields revealed strongly negative N*, positive Si*, and elevated Si:P ratios, indicating a system of acute nitrate scarcity but with residual phosphate and latent silicate availability. Phytoplankton communities were dominated by the cyanobacteria, Prochlorococcus, whose survival strategies included small functional absorption cross section of PSII ({sigma}PSII), enhanced PSII connectivity (p), highly elastic and reversible diel photophysiology that balanced high-light stress and nitrogen scarcity. Longer turnover times especially {tau}2 ({micro}s; PSII-PSI electron transport) seen in the region around 115{degrees} and 120{degrees}E and at 15{degrees}S, and during Cycles 3 and 4 are indicative of populations that were being stressed by Fe limitation as well. Our inference of Prochlorococcus is supported by complimentary measurements of flow cytometry, phytoplankton pigment composition and microscopy all of which confirmed the dominance of Prochlorococcus in these nutrient impoverished waters. Our observations further indicate that mesoscale eddies generated by ITF-SICC (South Indian Counter Current) interactions, can episodically shoal the nutricline, triggering transient pulses of larger eukaryotes. Collectively, these results demonstrate how acute nitrate depletion, compounded by Fe stress, structures a microbial community finely tuned to oligotrophy and capable of sustaining a short food chain involving appendicularians that directly support larval tuna. The Argo Basin therefore exemplifies how circulation-nutrient coupling shapes microbial communities and ecosystem function within a globally significant spawning habitat. Highlights1) Chronic nitrate limitation, with strongly negative N* and persistent N:P imbalance defines the Argo Basin while phosphate and silicate remain in relative excess. 2) Picocyanobacteria especially Prochlorococcus dominate the ecosystem, sustaining productivity under extreme oligotrophy through photophysiological strategies of reduced {sigma}PSII, enhanced PSII connectivity, and diel recovery from light stress. 3) Mesoscale eddies at the ITF-SICC front provide episodic relief, shoaling the nutricline and fueling transient pulses of larger phytoplankton that episodically reshape phytoplankton community structure and biomass 4) This oligotrophic-frontal seascape supports a short, efficient food web, enabling transfer of picophytoplankton to Southern Bluefin Tuna larvae via mainly appendicularians.

ecology↗

bioRxiv2025

Candida albicans infiltrates colon and rectal cancers causing therapeutic resistance and decreased survival

The microbiome is increasingly recognized as a modifier of cancer progression and therapy response, yet the role of intratumoral fungi remains poorly defined. Here, we identify Candida albicans colonization within human colorectal tumors as a predictor of reduced survival and impaired radiation response. Leveraging the Oncology Research Information Exchange Network (ORIEN) cohort, we show that high intratumoral Candida burden is associated with decreased survival across multiple gastrointestinal cancers, with the strongest treatment-specific effect in rectal cancer patients receiving radiotherapy. This observation was validated in independent rectal cancer cohorts using RNA sequencing and quantitative PCR. In immune-competent murine colorectal cancer models, oral gavage of C. albicans resulted in intratumoral colonization, accelerated tumor growth, and radiation resistance, effects not observed with Saccharomyces cerevisiae or PBS controls. Colonized tumors exhibited increased hypoxia, altered metabolic and transcriptional programs, and distinct expression of genes linked to cytokine signaling and cell survival. Hypoxia conditioned C. albicans secreted metabolites that directly conferred radiation resistance to colorectal cancer cells in vitro, implicating a cancer cell intrinsic mechanism independent of immune signaling. Untargeted metabolomics revealed enrichment of nucleosides and lipid oxidation intermediates under hypoxia, suggesting that C. albicans metabolites may provide substrates facilitating tumor recovery after irradiation. These findings establish C. albicans as a causal modifier of tumor biology and radiation response, highlighting intratumoral fungi as future potential therapeutic targets. Modulating fungal colonization or metabolism may improve radiotherapy outcomes and broaden our understanding of interactions between microbes and tumors.

cancer biology↗

bioRxiv2025

Insect-derived long non-coding RNAs function as epigenetic effectors to reprogram plant immunity

Cross-kingdom RNAs are emerging as critical mediators of interspecies interactions, yet the functions of long RNAs such as mRNAs and long non-coding RNAs (lncRNAs) in recipient organisms remain largely unexplored. Here, we show that the brown planthopper (Nilaparvata lugens, BPH), a major rice pest, translocates mRNAs and lncRNAs into rice plants, where they migrate systemically from feeding sites to distal tissues. Compared with BPH mRNAs, BPH Salivary gland Cross-kingdom LncRNA (BSCLs) exhibit markedly higher stability in rice. Among them, BSCL1 functions as a virulence factor that promotes BPH feeding and reproduction by suppressing host defense. Mechanistically, BSCL1 associates with the HIRA histone chaperone complex and displaces histone H3.3 from the promoters of transcription factors, including bHLH genes central to jasmonic acid signaling, thereby repressing transcriptional immunity. Our results identify BSCLs as systemic, RNA-based effectors that reprogram host defense at the epigenetic level, revealing a previously unrecognized mode of insect-mediated manipulation of plant immunity and highlighting lncRNAs as cross-kingdom regulators. Significance StatementPlant-herbivore interactions are traditionally viewed as battles over nutrients and defense signaling, mediated largely by proteins and small RNAs. Here, we demonstrate that long non-coding RNAs from brown planthopper saliva are translocated into rice, migrate systemically, and function as epigenetic effectors that suppress key transcription factors in jasmonic acid-mediated defense. Unlike insect mRNAs, these lncRNAs persist in the plant and reprogram immunity by interfering with histone deposition. This discovery uncovers a new class of mobile, RNA-based virulence factors, expands our understanding of cross-kingdom regulation, and suggests innovative strategies for pest control targeting RNA effectors.

plant biology↗

bioRxiv2025

Adaptations in Plasmodium tubulin determine unique microtubule architectures, mechanics and drug susceptibility

Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by which microtubule architecture varies through the life cycle of the malaria-causing parasite Plasmodium are not understood and provide a valuable framework for exploring how intrinsic properties of tubulin contribute to architectural variety. Using parasite-purified tubulin, we determined structures of P. falciparum microtubules by cryo-electron microscopy. Parasite-specific sequences change the tubulin dimer structure, thereby modifying drug susceptibility and polymer mechanical properties. Within the P. falciparum microtubule, lateral contacts are smaller but stronger, and the lattice is stiffer than in mammalian microtubules. Non-canonical microtubule architectures found in parasites are highly similar to those observed in vitro, validating the physiological relevance of these properties. Our findings show how evolutionary adaptation of tubulin modulates the material properties of the microtubule cytoskeleton.

biophysics↗

bioRxiv2025

Brain Preparedness for Active Forgetting: Cortisol Awakening Response Proacts Prefrontal Control Over Hippocampal-Striatal Circuitry

Stress-related psychiatric pathologies (e.g., rumination in depression, intrusive memories in PTSD) involve impaired inhibitory control over emotional memories and disrupted cortisol circadian rhythms. However, how these mechanisms interact to support adaptive forgetting remains unclear. Here, by integrating multi-modal neuroendocrine profiling with fMRI-based memory suppression in 90 participants, we demonstrate that the cortisol awakening response (CAR)--a circadian surge priming the brain for daily demands--proactively and selectively enhances suppression of recently acquired but not overnight-consolidated emotional memories. This time-dependent facilitation manifests through dual neural mechanisms: Robust CAR broadly amplifies dorsolateral prefrontal cortex (dlPFC) engagement during suppression attempts and specifically strengthens top-down dlPFC control over hippocampal-striatal circuits exclusively for recent traces. Our findings bridge circadian biology, systems neuroscience, and clinical psychopathology to establish CAR as a neuroendocrine preparedness mechanism that proactively configures adaptive forgetting circuits across sleep-wake cycles, thereby informing circadian-based interventions for stress disorders.

neuroscience↗

bioRxiv2025

PLiCat: Decoding protein-lipid interactions by large language model

MotivationProtein-lipid interactions are essential for many cellular processes, as proteins associate with diverse lipid molecules to exert distinct functions. However, existing approaches are limited in discriminating among lipid categories in these interactions. Recent advances in protein language models enable discovery of novel sequence insights. ResultsWe introduce PLiCat (Protein-Lipid interaction Categorization tool), a predictive framework designed to classify lipid categories interacting with proteins. By integrating ESMC and BERT models into a hybrid architecture, PLiCat achieves accurate and interpretable predictions to distinguish lipid-binding signatures across eight major lipid categories. Furthermore, we investigated the potential of PLiCat to identify lipid-binding sites and assess the impact of pathogenic mutations on lipid-binding events. Collectively, PLiCat provides a powerful framework for elucidating the lipid-binding codes, offering new opportunities for exploring lipid-binding specificity and guiding rational protein design. Availability and implementationThe PLiCat source code and processed datasets are available at https://github.com/Noora68/PLiCat.

bioinformatics↗