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Biology subjects

Fu, K.

Publications and source records attributed to Fu, K..

At least 19 recordsLinked to original sources

FiberPro 1.0: Multiagent AI-Guided Design for High-Throughput Production and Conformal Deposition of Functional Protein Micro/Nanofibers

Functional protein micro/nanofibers integrate high specific surface areas with bioactive architectures but remain hampered low production throughput and severe processing instability. Focused rotary jet spinning (FRJS) shows promising to break these throughput constraints while enabling direct, conformal deposition onto complex, irregular substrates. However, navigating FRJS's narrow processing windows in proteins remains failure-prone without closed-loop experimental guidance. Here, we report FiberPro 1.0, a large language model driven multi agent framework that unites high-throughput spinning with real-time experimental feedback for autonomous design, execution, and optimization. Across three protein systems, FiberPro 1.0 converged on spinnable formulations within an average of two iterations. To demonstrate high-throughput conformal deposition in a translational setting, FiberPro designed a zein-based active packaging system applied directly onto diverse food matrices. The resulting conformal coating combined potent antibacterial activity with real-time freshness monitoring, markedly suppressing Escherichia coli and extending shelf life. This work connects autonomous AI reasoning with high-throughput processing, establishing a verifiable route for scalable manufacturing and conformal coating of functional protein micro/nanofibers.

bioengineering↗

A neurofunctional signature of romantic love predicts rewards on social media, effects of oxytocin and drug-cue reactivity

Romantic love is a selective motivational state supporting pair bonding, yet its neural representation and relation to other affiliative-rewarding experiences remain unclear. Across eight fMRI studies (n=420) spanning naturalistic affiliative-reward, pharmacological and addiction-relevant experiments, we developed and evaluated multivariate whole-brain decoders of romantic love and friendship. Both signatures engaged mesocorticolimbic reward systems and the precuneus, yet were dissociable at the whole-brain level and in their recruitment of social-cognitive systems. The love signature generalized to reward on social media, was specific to positive valence, and did not track sweet-taste or monetary reward, indicating a distinct social-affiliative reward representation. Oxytocin selectively increased love - but not friendship - signature reactivity to the romantic partner. In an independent drug-cue-reactivity dataset, the love signature specifically identified heavy cannabis users. These findings establish a dissociable neurofunctional signature of romantic love in conserved bonding circuits that extend to digital affiliation and are co-opted in addiction.

neuroscience↗

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

Multidimensional variation and population stratification across 8000 complete human centromeres

Human centromeres are indispensable for the faithful segregation of chromosomes during cell division, yet their highly repetitive nature has historically precluded comprehensive characterization, leaving fundamental questions about their sequence diversity, evolution trajectories and function dynamics unresolved. Here, we generated 6,312 complete human centromere sequences from 320 phased genome assemblies in Asian Pan-Genome project phase 1. By integrating the assemblies from the Human Pangenome Reference Consortium (HPRC) and Human Genome Structural Variation Consortium (HGSVC), we constructed a multidimensional genetic variation map encompassing over 8,000 gapless centromeres. Centromeric satellite arrays account for 4.19% to 6.01% of the whole genome, with substantial variations in size and architecture across chromosomes. Using a refined alpha satellite clustering approach that captures global diversity, we identified 195 higher-order repeat (HOR) arrays, 56.4% of which are absent from the T2T-CHM13 reference genome. Extensive structural variations across multiple dimensions exhibit population stratification, including centromeric haplotypes (CenHaps), ultra-large pericentric inversions spanning up to 36.6 Mbp, and inter-chromosomal HOR sharing that reflects sequence exchange among chromosomes. Integrating CENP-A CUT&Tag experiments and long-read-based DNA methylation profiles, we demonstrate that 16.8% of centromeres harbor multiple potential kinetochore assembly sites, and CenHap-specific local HOR homogenization is associated with kinetochore positioning. Despite global suppression of recombination at centromeres, we observed asymmetric linkage disequilibrium flanking centromeres and an ancient recombination event within the centromere of chromosome 19. Furthermore, contrary to the prevailing assumption of high mutation rates in centromeres, our estimates based on stringent orthology reveal no significantly higher single-base substitution rates for centromeres relative to flanking pericentromeric regions with substantial variations across chromosomes, despite extraordinary structural plasticity. Collectively, these multi-scale centromeric variations provide a global view of human centromere diversity and population stratification, fundamentally redefine centromere evolution through a dual-track model balancing structural innovation with mutational constraint, and establish an essential resource for investigating centromere biology and a baseline reference for diagnosing centromere-associated disorders.

genomics↗

Platelets promote acute liver injury via extracellular vesicles-mediated Aldolase A

Platelets have emerged as active regulators of acute liver injury (ALI), yet the molecular mechanisms underlying their pathogenic functions remain poorly defined. Here, we demonstrate that platelets contribute to liver injury, in part, by metabolically reprogramming Kupffer cells (KCs). We show that platelets are actively recruited to the injured liver and communicate with KCs through extracellular vesicles (EVs), which deliver the glycolytic enzyme aldolase A (ALDOA) into recipient cells. This EV mediated transfer promotes glycolytic reprogramming in KCs, contributing to their proinflammatory activation and amplification of hepatic injury. Genetic ablation of Aldoa in platelets attenuated liver injury, demonstrating a pathogenic role for platelet derived ALDOA in vivo. Pharmacological inhibition of ALDOA with Aldometanib markedly attenuated liver injury. Circulating ALDOA levels were elevated in patients with ALI and correlated with disease severity. These findings uncover a platelet macrophage metabolic axis that drives ALI and nominate ALDOA as a therapeutic target and biomarker.

pathology↗

The abnormal C-terminus in DVL1 impacts Robinow Syndrome phenotypes

Robinow Syndrome is a polygenic, rare skeletal disorder characterized by craniofacial and limb defects. The genes involved are in the Wingless-related Integration site-1 (WNT) pathway and DVL1 (Dishevelled 1) is the most commonly affected gene. In all pathogenic variants of DVL1, a frameshift replaces the C terminus with a novel peptide. We tested whether the variant DVL11519{Delta}T was sufficient to alter development in vivo and in vitro in two animal models. We compared phenotypes to wtDVL1 or DVL1 with a stop codon at position 1519. Misexpression of DVL11519{Delta}T in the developing face of chicken embryos with an avian retrovirus, leads to a widening of the frontonasal mass similar to the human facial phenotype and ultimately to inhibition of skeletogenesis that was also verified in primary cultures of frontonasal mass mesenchyme. In luciferase assays carried out in facial mesenchyme, the wtDVL1 activated canonical and JNK PCP WNT signalling however the DVL11519* and the DVL11519{Delta}T variant removed some but not all of the signaling activity. We also determined that there is mislocalization of the protein expressed from DVL11519{Delta}T in the nucleus while the other two constructs were mainly found in the cytoplasm. In complementary Drosophila experiments using a variety of readouts, only the DVL11519{Delta}T variant impacted morphogenesis and signaling. This is the first study to clarify the pathogenesis of Robinow syndrome is due to the novel C-terminus of DVL1 which exerts dominant interference on morphogenesis, skeletogenesis and WNT signaling.

developmental biology↗

Shared and distinct default mode systems in mental time travel and affective experience over time

Overarching conceptualizations propose a critical role of the default mode network (DMN) in self-referential mental time travel, particularly in autobiographical memory retrieval and episodic future thinking, and internal (intrinsic) emotion generation and regulation. However, these conceptualizations have not been directly evaluated. Against this background, the present fMRI study aimed to identify both shared and distinct neural systems underlying autobiographical episodic processing across different temporal contexts - specifically, episodic memory retrieval (EMR) and episodic future thinking (EFT) - and to examine how these systems interact with affective experiences, including valence and arousal. Our findings demonstrated the central role of the DMN - encompassing the medial prefrontal cortex (mPFC), posterior cingulate cortex (PCC), and medial temporal lobe (MTL) - in both EMR and EFT. Importantly, we identified a functional dissociation along both valence and temporal dimensions: the ventromedial prefrontal cortex (vmPFC) was more strongly associated with positive experiences and simulations, whereas the dorsomedial prefrontal cortex (dmPFC) was consistently engaged during the processing of negative affect across past and future contexts. Moreover, representational similarity and parametric analyses indicated that the hippocampus supports differential processing of valence and arousal across temporal domains. Together, these findings provide empirical evidence for the involvement of cortical midline core DMN systems in autobiographical processing across time and suggest overlapping and distinct systems for the integration of emotional experiences across mental time travel.

neuroscience↗

Real-time functional connectivity-based neurofeedback of the DLPFC-amygdala pathway during threat-exposure attenuates anxiety

BackgroundAdaptive regulation of negative emotion is vital for mental health and dysregulations in this domain contribute to the major mental disorders, including anxiety and depression. On the neural level, efficient emotion regulation has been linked to functional communication between the dorsolateral prefrontal cortex (DLPFC) and the amygdala. Gaining voluntary control over this pathway may present an effective strategy for potentiating emotion regulation. ObjectiveAgainst this background, we developed a novel connectivity-based real-time fMRI (rt-fMRI) neurofeedback (NF) training that enables individuals to gain volitional control over the DLPFC-amygdala pathway during exposure to threatening stimuli. MethodsThe study employed a pre-registered, randomized, sham-controlled design with the experimental group (n = 22) receiving real-time NF information on connectivity between the right DLPFC and the amygdala during threat exposure and the sham control group (n = 23) receiving connectivity NF from a circuit not related to emotion regulation. The ability to maintain regulatory control in the absence of feedback was assessed after four NF runs. Primary outcomes included functional connectivity of the target pathway, as well as anxiety scores. ResultsThe results demonstrate that successful acquisition of self-regulation of the rDLPFC-amygdala top-down regulatory circuit in the experimental NF group facilitated attenuation of anxiety. ConclusionIn summary, our findings suggest that real-time fMRI neurofeedback (rtfMRI-NF) allows to volitionally enhance rDLPFC-amygdala connectivity, and in turn reduces negative emotional states, rendering the training a promising neurotechnology intervention for mental disorders.

neuroscience↗

Cytoplasmic Abundant Heat-Soluble Proteins from Tardigrades Protect Synthetic Cells Under Stress

Cytoplasmic abundant heat-soluble (CAHS) proteins, a stress-responsive intrinsically disordered protein from tardigrades, have been discovered to form gel-like networks providing structural support during dehydration, thus enabling anhydrobiosis. However, the mechanism by which CAHS proteins protect the dehydrating cellular membrane remains enigmatic. Using giant unilamellar vesicles (GUVs) as a model membrane system, we show that encapsulated CAHS12 undergoes a reversible structural transformation that reinforces membrane integrity and preserves encapsulated components, mimicking natural anhydrobiosis. CAHS12-containing GUVs demonstrated stability for weeks and mechanical robustness under dehydration, elevated temperature, and osmotic stresses. Molecular simulations suggest that CAHS12 forms a filamentous network within the vesicle lumen that mitigates membrane collapse and preserves compartmental architecture. Synthetic cells with cell-free transcription-translation capabilities withstand desiccation and recover biochemical activities, akin to the tun state of the tardigrade. This discovery opens up synthetic cell applications in bioengineering, cold-chain-independent biomanufacturing, and adaptive biointerfaces.

synthetic biology↗

Functional genomics and tumor microenvironment analysis reveal prognostic biological subtypes in Mantle cell lymphoma

Mantle cell lymphoma (MCL) is a genetically and clinically heterogeneous B-cell malignancy. We studied two MCL cohorts with differing treatment patterns: one enriched for immunochemotherapy, the other for chemotherapy alone. TP53 alterations were consistently associated with poor prognosis, whereas ATM mutations correlated with improved outcomes following rituximab-based chemotherapy. Based on recurrent genetic events, six clusters were identified and refined into three prognostic groups: high-risk (TP53 mutations and deletions at 17p13.3, 13q14.2, and 19p13.3), intermediate-risk (ATM and epigenetic regulator mutations, or gains at 8q/17q/15q), and low-risk (lacking TP53 alterations, rare ATM mutations without 11q deletions, gains at 3q, deletions at 6q). Transcriptomic analysis revealed enrichment of proliferation, metabolism-promoting gene signatures in high-risk; angiogenesis and NOTCH signaling in intermediate-risk; and proinflammatory-related (i.e., IFN, TNF) in low-risk MCLs. Multi-proteomic spatial profiling using imaging mass cytometry (IMC) demonstrated enrichment of CD8 T cells with high expression of exhaustion markers and dominant population of myeloid cells skewed toward an M2-like phenotype. Compared to ATM-perturbed tumors, TP53-perturbed tumors exhibited enriched SOX11 tumor cells and enhanced tumor-immune cell interactions. Functional analysis revealed that p53 represses BCR signaling through PTPN6 activation. Collectively, these findings highlight distinct molecular and immune landscapes and reveal therapeutic vulnerabilities in high-risk TP53-altered MCL.

cancer biology↗

FoldMark: Protecting Protein Generative Models with Watermarking

Proteins are the principal architects of life, fueling advances in bioengineering, drug discovery, and synthetic biology. The integration of generative AI with computational protein science has revolutionized protein design while also posing dual-use risks, such as enabling the creation of pandemic-capable proteins that require strong biosecurity safeguards. Here, we introduce FoldMark, a first-of-its-kind watermarking strategy leveraging distributional and evolutionary principles tailored for protein generative models, balancing watermark capacity and structural quality. FoldMark achieves over 95% watermark bit accuracy at 32 bits with minimal impact on structural quality (>0.9 scTM scores) for leading models including AlphaFold3, ESMFold, RFDiffusion, and RFDiffusionAA. For user tracing, FoldMark can successfully trace up to 1 million users. To validate FoldMark in wet lab, we applied it to structure-based design of EGFP and CRISPR-Cas13, showing wildtype-level function (98% fluorescence, 95% editing efficiency) and >90% watermark detection, demonstrating its practical utility for safeguarding AI-driven protein research.

bioinformatics↗

Signatures of social pain empathy: general and process-specific brain-wide representations of social exclusion and separation

Empathy can be elicited by physiological pain, as well as in social contexts. Although physiological and different social contexts induce a strong subjective experience of empathy, the general and context-specific neural representations remain elusive. Here, we combine fMRI with multivariate pattern analysis to establish neurofunctional models for pain empathy triggered by social exclusion and separation. Our findings revealed both overlapping and distinct neural representations for social exclusion and separation empathy across cortical and subcortical regions. This study established an evolutionary model that traces the progression from social pain to physiological pain empathy. In conclusion, this study establishes neural decoding models for pain empathy evoked by social exclusion and social separation, revealing their neural foundations and interconnectedness of empathy induced by social and physiological stimuli. These findings deepen our understanding of the neurobiological mechanisms underlying social pain empathy and provide robust neuromarkers to precisely evaluate empathy across physiological and social domains.

neuroscience↗

Distinct neural computations scale the violation of expected reward and emotion in social transgressions

Traditional decision-making models conceptualize humans as optimal learners aiming to maximize outcomes by leveraging reward prediction errors (PE). While violated emotional expectations (emotional PEs) have recently been formalized, the underlying neurofunctional basis and whether it differs from reward PEs remain unclear. Using a modified fMRI Ultimatum Game on n=43 participants we modelled reward and emotional PEs in response to unfair offers and subsequent punishment decisions. Computational modelling revealed distinct contributions of reward and emotional PEs to punishment decisions, with reward PE exerting a stronger impact. This process was neurofunctionally dissociable such that (1) reward engaged the dorsomedial prefrontal cortex while emotional experience recruited the anterior insula, (2) multivariate decoding accurately separated reward and emotional PEs. Predictive neural expressions of reward but not emotional PEs in fronto-insular systems predicted neurofunctional and behavioral punishment decisions. Overall, these findings suggest distinct neurocomputational processes underlie reward and emotional PEs which uniquely impact social decisions.

neuroscience↗

Differentiating erythroblasts adapt to turbulent flow by accelerating maturation and activating cholesterol biosynthesis.

In vitro culture of erythroblasts (EBL) and production of mature erythrocytes for transfusions requires upscaling in fluidic-turbulent bioreactors, resulting in membrane shear stress. For the implementation of erythroid cultures in bioreactors, understanding the effects of mechanical stress on terminal EBL differentiation is required. To this end, we investigated the effect of orbital shaking-induced shear stress on differentiating CD49d+CD235low primary human EBL towards enucleated reticulocytes at the molecular, cellular, and functional level. Orbital shaking at the onset of EBL differentiation enhanced cell maturation increasing enucleation percentage compared to static cultures, without cell viability loss. Transcriptome analysis uncovered 505 genes differentially expressed between static and dynamic cultures, with genes involved in lipid and cholesterol biosynthesis upregulated in dynamic conditions. In line with this, cells differentiated in orbital-shakers showed increased cholesterol concentration and osmotic resistance compared to static cultures. HMGCR (3-Hydroxy-3-Methylglutaryl-CoA-Reductase), rate-limiting enzyme of the cholesterol biosynthesis pathway, showed earlier and significantly higher induction during differentiation in dynamic. The severe loss of EBL in dynamic, but not in static conditions, due to HMGCR inhibition confirmed the ability of EBL to adapt to shear stress through modulating of their transcriptional program and upregulation of cholesterol biosynthesis. This work sheds light into specific mechanisms that will assist the successful upscaling of erythroid differentiation in turbulent bioreactors. In addition, as shear-stress on hematopoietic cells is also occurring within the bone marrow niche, these results introduces a potential novel signalling axis that need to be integrated into the known transduction pathways that control erythropoiesis.

cell biology↗

Functional genomics in chicken embryos reveal the pathogenicity of two missense FZD2 variants associated with dominant Robinow syndrome

Robinow syndrome (RS) is a rare disease caused by mutations in seven WNT pathway genes. Features include craniofacial widening and jaw hypoplasia. We used the chicken embryo to test two autosomal dominant RS (ADRS) missense FZD2 variants on the frontonasal mass, the affected region in RS. The wild-type (wt) and variant hFZD2 inhibited beak ossification. The bone hypoplasia was possibly mediated by decreased levels of WNT and BMP pathway genes. In primary cultures, hFZD2 variants inhibited chondrogenesis, increased nuclear shuttling of {beta}-catenin and increased expression of TWIST1, both known to suppress chondrogenesis. In luciferase reporter assays, proteins coding for 1301G>T and 425C>T FZD2 variants weakly activated canonical WNT reporter and dominantly interfered with wtFZD2. In the JNK-PCP WNT pathway luciferase assay, only the 425C>T showed a loss-of-function. The 1301G>T variant presumably acts through a JNK-independent pathway. This is the first study to demonstrate that the ADRS-FZD2 missense variants cause craniofacial and WNT signaling defects. Frontonasal mass width is increased by both hFZD2 variants which sheds light on the ontogeny of the broad facial features seen in individuals with RS. Summary StatementGain-of-function studies on FZD2 missense variants associated with Robinow syndrome led to increased facial width, altered Wnt signaling and inhibition of beak skeletogenesis in chicken embryos.

developmental biology↗

Real-Time Spatiotemporal Measurement of Extracellular Signaling Molecules Using an Aptamer Switch-Conjugated Hydrogel Matrix

Cells rely on secreted signaling molecules to coordinate essential biological functions including development, metabolism, and immunity. Unfortunately, such signaling processes remain difficult to measure with sufficient chemical specificity and temporal resolution. To address this need, we have developed an aptamer-conjugated hydrogel matrix that enables continuous fluorescent measurement of specific secreted analytes - in two dimensions, in real-time. As a proof of concept, we performed real-time imaging of Dictyostelium discoideum cells, a well-studied amoeba model wherein inter-cellular communication is performed though cAMP signaling. We engineered a set of aptamer switches that generate a rapid and reversible change in fluorescence in response to cAMP signals. By combining multiple switches with different dynamic ranges, we can measure cAMP concentrations spanning three orders of magnitude in a single experiment. These sensors are embedded within a biocompatible hydrogel on which cells are cultured and their cAMP secretions can be imaged using fluorescent microscopy. Using this aptamer-hydrogel material system, we achieved the first direct measurements of oscillatory cAMP signaling that correlate closely with previous indirect measurements. Using different aptamer switches, this approach could be generalized for measuring other secreted molecules to directly visualize diverse extracellular signaling processes and the biological effects that they trigger in recipient cells.

bioengineering↗

Transcriptomic profiling of the adult reptilian dentition sheds light on the genes regulating indefinite tooth replacement

The aim of this study is to profile the transcriptome of teeth and the surrounding tissues of an adult lizard dentition (Eublepharis macularius) that is actively replacing teeth throughout life. Bulk RNAseq was used to compare teeth that are in function versus unerupted, developing teeth and single cell RNA-seq was carried out on jaw segments containing the dental forming tissues. In bulk RNAseq data, we found that functional teeth expressed genes involved in bone and tooth resorption. Indeed, multinucleated odontoclasts were abundant in tissue sections of functional teeth undergoing resorption. Unexpectedly, chemotaxis gene SEMA3A was expressed within odontoblasts and in adjacent mesenchyme, confirmed using RNAscope. Semaphorins may be involved in regulating odontoclasts during tooth resorption. The scRNA-seq experiment successfully isolated dental mesenchyme and epithelial cells. We confirmed that some of these genes are expressed in the earliest tooth buds within the tooth forming field. In addition, we found evidence of convergent evolution in the tooth eruption trait. Geckos evolved a means for second generation teeth to communicate with the functional teeth. Instead of a dental follicle inducing an eruption pathway as in the mammal, the gecko and other squamate reptiles use the enamel organ of the successional teeth to trigger tooth resorption of the functional teeth, thus creating an eruption pathway. New molecules such as SEMA3A and SFRP2 may also participate in this process. Future studies on the gecko will uncover the molecular basis of convergent evolution in the dentition.

evolutionary biology↗

Sphingosine kinases promote Ebola virus infection and can be targeted to inhibit filoviruses, coronaviruses, and arenaviruses using late endocytic trafficking to enter cells

Entry of enveloped viruses in host cells requires the fusion of the viral and host cell membranes, a process that is facilitated by viral fusion proteins protruding from the viral envelope. For fusion, viral fusion proteins need to be triggered by host factors and for some viruses, such as Ebola virus (EBOV) and Lassa fever virus, this event occurs inside endosomes and/or lysosomes. Consequently, these late-penetrating viruses must be internalized and delivered to entry-conducive intracellular vesicles. Because endocytosis and vesicular trafficking are tightly regulated cellular processes, late penetrating viruses also depend on specific host factors, such as signaling molecules, for efficient viral delivery to the site of fusion, suggesting that these could be targeted for antiviral therapy. In this study, we investigated a role for sphingosine kinases (SKs) in viral entry and found that chemical inhibition of sphingosine kinase 1 (SK1) and/or SK2 and knockdown of SK1 or SK2, inhibited entry of EBOV into host cells. Mechanistically, inhibition of SK1 and/or SK2 prevented EBOV from reaching late-endosomes and lysosomes that are positive for the EBOV receptor, Niemann Pick C1 (NPC1). Furthermore, we present evidence that suggests the trafficking defect caused by SK1/2 inhibition occurs independently of S1P signaling through cell-surface S1PRs. Lastly, we found that chemical inhibition of SKs prevents entry of other late-penetrating viruses, including arenaviruses and coronaviruses, in addition to inhibiting infection by replication competent EBOV and SARS-CoV-2 in Huh7.5 cells. In sum, our results highlight an important role played by SKs in endocytic trafficking which can be targeted to inhibit entry of late-penetrating viruses. SK inhibitors could serve as a starting point for the development of broad-spectrum antiviral therapeutics.

microbiology↗