Biology subjects

Cui, D.

Publications and source records attributed to Cui, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Chaperonin recognition of protein dynamics drives drug resistance

The emergence of drug resistance is typically driven by mutations that alter drug-target affinity, yet the role of host cellular machinery regulating these processes remains unclear. Here, we reveal that the chaperonin GroEL/S promotes drug resistance through recognition of protein dynamics. Using directed evolution of E. coli DHFR under antibiotic stress and varying GroEL/S expression, we identify a well-folded resistance variant whose fitness, despite tight inhibitor binding, is critically potentiated by GroEL/S engagement. X-ray crystallography, NMR, molecular dynamics and kinetic modeling reveal that millisecond-timescale flipping of the M20 loop generates steric accessibility and a kinetic window for chaperonin interaction that forcibly displaces tightly bound inhibitors, thereby overriding thermodynamic equilibrium of inhibitor binding to restore the active enzyme pool and preserve metabolic flux. Our findings not only reveal a novel paradigm of "dynamic recognition" where both conformational kinetics and distribution govern chaperonin recognition but also establish chaperonins as "deligandases" that actively modulate in vivo drug binding, suggesting that chaperone surveillance of the cellular proteome extends beyond quality control to govern native protein function. This mechanism defines a previously unrecognized route for the rapid development of drug resistance, with implications for understanding therapeutics of microbial infections and human malignancies.

biophysics↗

bioRxiv2026

Endolysosomal damage promotes intraluminal protein condensate formation that limits cytosolic leakage

Endolysosomal membrane damage is a detrimental process in mammalian cells that results in leakage of the luminal contents into the cytosol. However, the nature and extent of the leakage during membrane damage is unknown. Here, we show that endomembrane damage induces the rapid formation of intraluminal condensates in endolysosomes. A subset of resident luminal proteins undergo spatially coordinated condensation upon endomembrane damage. Electron microscopy reveals distinct luminal morphology, and cryo-electron tomography confirms the condensed ultrastructure in their native state. Condensate formation occurs across mechanistically distinct modes of membrane injury and is reversibly dissociated upon lysosomal recovery. Remarkably, these condensates impose a previously unrecognised barrier to endolysosomal escape of therapeutic oligonucleotides. Despite endomembrane damage, luminal oligonucleotide therapeutics are sequestered in damaged endolysosomes through condensate-mediated biophysical immobilisation. Targeting condensate sequestration could represent a novel strategy to improve oligonucleotide-based therapeutics.

cell biology↗

bioRxiv2026

Automated Multimodal Correlative Registration for Organelle-Specific Molecular Imaging

Mapping subcellular drug distribution is essential for understanding trafficking and off-target effects. NanoSIMS enables chemical imaging of labeled therapeutics, but signal interpretation requires ultrastructural correlation with electron microscopy, a manual and laborious process. We present an automated AI-driven pipeline for correlating chemical and ultrastructural images, enabling multiscale, organelle-precise imaging of molecules in cells and tissues. The method integrates bidirectional optical flow, confidence-guided affine transformation, and automated template matching for cross-scale EM alignment. Morphology-rich ion channels (e.g., 32S) estimate transformations that propagate to sparse therapeutic signals (e.g., 79Br, 15N), overcoming low signal-to-noise challenges. We validate this framework across diverse cell and tissue types, tracking oligonucleotide and antibody therapeutics in vitro and in vivo to reveal cell-type- and organelle-specific distribution patterns. This work establishes a generalizable platform for automated multimodal registration and organelle-resolved subcellular pharmacology.

bioinformatics↗

bioRxiv2026

Facilitating NMR Resonance Assignment with Metabolic Tampering

The ability to assign amino acid resonances in multidimensional NMR spectra of biomolecules is necessary for detailed studies of protein structure and dynamics. Despite creative advances in isotopic labeling, unlabeling and multidimensional NMR experiments, resonance assignment remains a bottleneck in studies of large proteins. In this work, we show that the metabolic flux through biosynthetic pathways of amino acid production during protein expression can be modulated to aid in the identification of resonances in two-dimensional NMR spectra. This straightforward method involves doping 15N-enriched minimal media with small amounts of rich natural abundance media to generate unique peak intensity attenuation patterns, producing type-specific signatures of amino acids in two-dimensional 15N HSQC experiments. Using three model proteins, IGPS (51 kDa heterodimer), PTP1B (35 kDa), PHPT1 (14 kDa), we show that this method can disentangle several amino acid types, is robust to different expression conditions, and is a useful supplement for triple resonance experiments in protein backbone resonance assignments.

biochemistry↗

bioRxiv2025

The biochemical nature of senile plaques: intracellular destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials

The pathological mechanism of senile plaque formation in Alzheimers disease remains a challenging unresolved problem for over one hundred years. In this study, we investigated senile plaque pathogenesis based on immunohistochemistry, fluorescence imaging and quantitative analysis of AD front brain sections with multiple senile plaque related markers such as A{beta}, MAP2, phos-Tau, Cathepsin D, Sortilin 1, Ceruloplasmin and Hemin. Firstly, we confirmed that senile plaque A{beta} deposition mostly happened in MAP2-positive but degenerative neuritic processes. Secondly, we found an interesting dual-component granular or diffusive staining pattern of all of these senile plaque related markers, matching to two states of lysosomes, relatively-stable granule lysosomes and destabilized diffusive lysosomes as shown by lysosome-related marker Cathepsin D or Sortilin 1 staining. Thirdly, dystrophic senile plaque neural processes contain hemorrhage-related markers such as Ceruloplasmin and Hemin. In addition, A{beta} deposition, Tau phosphorylation, lysosome destabilization are all enriched at the sites of microaneurysm formation. Moreover, senile plaques are also characterized by a widespread binary phos-Tau staining pattern with difference in term of staining intensity. We concluded that senile plaques are formed by destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials, with microaneurysm as an important intermediate stage.

cell biology↗

bioRxiv2025

A Context-Sensitive Neural Hierarchy for Evaluating Temporal Structure in Primate Vocalizations

Understanding how the brain encodes temporal order in communication is central to explaining how complex interactions are perceived as coherent events. In humans, disrupting the sequence of words or scenes abolishes characteristic activity in higher-order networks, but whether similar mechanisms exist in nonhuman primates remains unknown. Here we used ultra-high-field fMRI (9.4 T) in awake marmosets to test how the marmoset brain evaluates temporal structure in natural conspecific vocalizations. Animals heard vocal sequences from three social contexts (angry, conversational, food-related) presented in intact, reversed, or randomized order, with call identity held constant. Disrupting sequence order altered responses across a distributed cortical-subcortical network. Contrast to reversed order, intact sequences drove stronger activation in prefrontal, cingulate, parietal, and somatosensory regions, whereas randomization produced the most widespread disruptions, additionally recruiting motor, insular, hippocampal, and thalamic territories. Uni- and multivariate analyses revealed a core network--including prefrontal area 8, cingulate areas 24/32, somatosensory cortex, and parietal Tpt--consistently sensitive to temporal coherence, with broader recruitment under severe disruption. Network-level dynamics further varied by context: conversation elicited earlier sensitivity to sequence disruptions, angry peaked later, and food built more gradually. These findings provide the first whole-brain evidence that marmosets engage hierarchically organized, context-sensitive networks to evaluate multi-agent vocal sequence structure, establishing a cross-species bridge to human narrative processing.

neuroscience↗

bioRxiv2025

The translation initiation factor DHX29 appears to pull on mRNA in a direction opposite to scanning.

The DExH-box helicase DHX29 plays a critical role in mammalian translation initiation. It is required for the scanning of mRNAs with complex 5UTRs. Despite its importance, the detailed mechanism of DHX29s action has remained debated. Using structural models derived from AlphaFold and cryo-EM structure of DHX29 bound to the ribosomal 43S pre-initiation complex, we provide a revised structural framework that clarifies the interplay between DHX29, the 40S ribosomal subunit, and eIF3. Our findings suggest that the 40S subunit regulates DHX29s NTPase activity through an activation mechanism resembling the G-patch protein regulation of DEAH helicases. Moreover, our model supports a 3 to 5 translocase mechanism, in which DHX29 transiently pulls the mRNA opposite to the scanning direction, destabilizing stable stem-loops trapped in the mRNA channel and allowing scanning to resume. This structural analysis refines our understanding of DHX29s function and provides new hypotheses regarding its role in mRNA unwinding during scanning and start codon selection.

biophysics↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Controllable Gap Junctions by Vitamin B12 and Light

Gap junctions, mediate rapid signal transduction between contiguous cells, which are indispensable for multicellular organisms to coordinate cellular activities across numerous physiological processes. However, precise control of gap junctions remains elusive. Herein, we present CarGAP, a single-component chemo-optogenetic tool that utilizes the C-terminal adenosylcobalamin (AdoB12) binding domain of a photoreceptor protein (i.e., CarHC) to achieve reversible control over both vertebrate and invertebrate gap junctions with spatiotemporal precision. The vertebrate CarGAP (i.e., Cx-CarGAP), created by genetically fusing connexins with CarHC in mammalian cells, can efficiently block the gap junction channels through AdoB12-induced protein oligomerization, and subsequently reinstate them via green light-induced protein disassembly. We further introduced the CarGAP system (i.e., Inx-CarGAP) to the Drosophila ovary, enabling reversible control over the heterotypic gap junctions formed by innexin2 (Inx2) and innexin4 (Inx4, also known as zero population growth, Zpg), thereby uncovering the roles of gap junctions in stem cell-niche interactions. This study illustrates CarGAP as a generalizable chemo-optogenetic tool for interrogating the functions of gap junctions in various biological contexts.

bioengineering↗

bioRxiv2024

BOOST: a robust ten-fold expansion method on hour-scale

Expansion microscopy (ExM) enhances the microscopy resolution by physically expanding biological specimens and improves the visualization of structural and molecular details. Numerous ExM techniques and labeling methods have been developed and refined over the past decade to cater to specific research needs. Nonetheless, a shared limitation among current protocols is the extensive time required for sample processing, particularly for challenging-to-expand biological specimens (e.g., formalin-fixed paraffin-embedded (FFPE) sections and large three-dimensional specimens). Here, we have developed a rapid and robust ExM workflow named BOOST, which leverages a series of novel microwave (MW)-accelerated ExM chemistry, resulting in a single-step linear expansion of [~]10x. Specifically, BOOST facilitates a [~]10-fold expansion of cultured cells, tissue sections, and even the challenging-to-expand FFPE sections under merely 90 minutes with heat and surfactant-based protein denaturation. Furthermore, BOOST employs microwave-assisted proteomic staining and immunostaining to facilitate high-resolution visualization of structural and molecular details with significantly enhanced throughput. Noteworthily, BOOST has pioneered a [~]10-fold expansion of large millimeter-sized three-dimensional specimens in approximately three hours. BOOST offers an easily adaptable workflow based on stable and common reagents, thus boosting the potential adoption of ExM methods in biological investigations.

bioengineering↗

bioRxiv2024

Pathological axonal enlargement in connection with amyloidosis, lysosome destabilization and hemorrhage is a major defect in the Alzheimer's disease

AbstractAlzheimers disease (AD) is a multi-amyloidosis disease with A{beta} deposits in the cerebral blood vessels, microaneurysms and senile plaques. How A{beta} amyloidosis affects axon pathology is not well-examined. We studied A{beta}-related axonal phenotypes with histochemistry, immunohistochemistry and fluorescence imaging methods. Widespread axonal amyloidosis with distinctive axonal enlargement was observed in AD. A{beta}-positive axon diameters in AD brains were 1.72 times of control brain axons by average. Axonal amyloidosis also associated with MAP2 reduction, Tau phosphorylation, lysosome destabilization and hemorrhagic markers such as ApoE, HBA, HbA1C and Hemin. Lysosome destabilization in AD was also clearly identified in the neural soma, associating with the co-expression of A{beta} and Cathepsin D, HBA, ACTA2 and ColIV, implicating exogeneous hemorrhagic protein intake might influence neural lysosome stability. The data showed that A{beta}-containing lysosomes were 2.23 times as large as the control lysosomes. Furthermore, under rare conditions, axon breakages were observed, which likely resulted in Wallerian degeneration. In summary, axonal enlargement associated with amyloidosis, chronic microhemorrhage and lysosome destabilization is a major defect in Alzheimers disease.

cell biology↗

bioRxiv2024

Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3',5'-hydroxylase

Flavonoids in Musaceae are involved in pigmentation and stress responses, including pathogen defense and UV protection, and are a component of the healthy human diet. Identification and analysis of the sequence and copy number of flavonoid biosynthetic genes are valuable for understanding the nature and diversity of flavonoid evolution in Musaceae species. In this study, we identified 71 to 80 flavonoid biosynthetic genes in chromosome-scale genome sequence assemblies of Musaceae, including those of Ensete glaucum, Musella lasiocarpa, Musa beccarii, M. acuminata, M. balbisiana, and M. schizocarpa, checking annotations with BLAST and determining the presence of conserved domains. The number of genes increased through segmental duplication and tandem duplication. Orthologues of both structural and regulatory genes in the flavonoid biosynthetic pathway are highly conserved across Musaceae. The flavonoid 3,5-hydroxylase gene F35Hs was amplified in Musaceae and ginger compared with grasses (rice, Brachypodium, Avena longiglumis, and sorghum). One group of genes from this gene family amplified near the centromere of chromosome 2 in the x = 11 Musaceae species. Flavonoid biosynthetic genes displayed few consistent responses in the yellow and red bracts of Musella lasiocarpa when subjected to low temperatures. The expression levels of MlDFR2/3 increased while MlLAR was reduced by half. These results establish the range of diversity in both sequence and copy number of flavonoid biosynthetic genes during evolution of Musaceae. The combination of allelic variants of genes, changes in their copy numbers, and variation in transcription factors with the modulation of expression under cold treatments and between bract-colours suggests the variation may be exploited in plant breeding programmes, particularly for improvement of stress-resistance in the banana crop.

genetics↗

bioRxiv2023

High-resolution ultrastructure and morphology of marine ammonia-oxidizing archaea Nitrosopumilus maritimus SCM1 revealed by Cryo-ET and STEM-EDS

Nitrososphaerota, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their significance in Earths ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant question unanswered of how the machinery of these organisms underpins metabolic functions. In this study, we combined chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaerota. Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules in which one type is possibly composed of polyphosphate, while the other type is polyhydroxyalkanoate. Collectively, these findings provide visual evidence for the resilience of AOA in the vast oligotrophic marine environment.

microbiology↗

bioRxiv2023

Aβ-aggregation-generated blue autofluorescence illuminates senile plaques, complex blood and vascular pathologies in the Alzheimer's disease

Senile plaque blue autofluorescence in the Alzheimers disease (AD) was discovered around 40 years ago, however, its impact on AD pathology is not fully examined. We analyzed senile plaques with immunohistochemistry and fluorescence imaging on AD brain pathological sections and also the A{beta} aggregation process in vitro in test tubes. In DAPI or Hoechst staining experiments, the data showed that the nuclear blue fluorescence could only be correctly assigned after subtracting the blue autofluorescence background. The plaque cores have very strong blue autofluorescence which is roughly 2.09 times of average DAPI nuclear staining and roughly 1.78 times of average Hoechst nuclear staining. The composite flower-like structures formed by Cathepsin D lysosomal staining wrapping dense core blue fluorescence should not be considered as central-nucleated neurons filled with defective lysosomes since there was no nuclear staining in the plaque core when the blue autofluorescence was subtracted. Furthermore, the dense cores were shown to be completely lack of nuclear signals by PI staining. The A{beta} aggregation assay indicated that both A{beta} self-oligomers and A{beta}/Hemoglobin (Hb) heterocomplexes had significant blue autofluorescence. However, the blue autofluorescence intensity was not always proportional to the intensity of A{beta} immunostaining. The majority of aggregates in the A{beta}/Hb incubations were sensitive to Proteinase K (PK) digestion while the rest were PK resistant. The blue autofluorescence of A{beta} aggregates not only labels senile plaques but also illustrates red blood cell aggregation, hemolysis, CAA, vascular amyloid plaques, vascular adhesion and microaneurysm. In summary, we conclude that A{beta}-aggregation-generated blue autofluorescence is an excellent amyloid pathology marker in the senile plaques, blood and vascular pathologies in the Alzheimers disease.

cell biology↗

bioRxiv2023

The Neonatal Gyrencephalic Cortex Maintains Regionally Distinct Streams of Neuroblasts

Neurodevelopmental mechanisms have evolved to support the formation of diverse brain structures, such as in humans, during the perinatal period. Here, we demonstrate that neonatal gyrencephalic brains harbor an expanded subventricular zone, termed the Arc, defined by tiered arrangement of doublecortin (DCX)-expressing neuroblasts and vascular enrichment at the ventricular wall. The Arc is the origin of dorsal and ventral populations of migratory neuroblasts that target multiple regions involved in higher cognitive functions. Arc-derived migratory streams, primarily from the caudal ganglionic eminence, are composed of diverse neuronal subtypes with distinct spatial and migratory-receptor profiles. Our findings indicate the Arc is a structure present in phylogenetically divergent species that supports the expansion of postnatal neuronal migration, contributing to a protracted formation of cortical circuits in gyrencephalic brains. One-Sentence SummaryThe ventricular cytoarchitecture of gyrencephalic brains supports an ongoing supply of migratory neurons to the neonatal cortex.

neuroscience↗

bioRxiv2023

Re-evaluating the nuclear staining on pathological sections in Alzheimer's disease

A paper recently published on Nature Neuroscience, asserting that lysosome leakage induces neuronal cell death and the formation of senile plaques in Alzheimers disease. The study believed that flower-like perikaryal rosettes formed by packed autophagic vacuoles around central nuclei, termed "PANTHOS" neurons, are responsible for the senile plaque formation. However, all of the nuclei staining in this paper based on images in the blue fluorescence channel. We did detailed studies on the senile plaque blue autofluorescence and found that senile plaque blue autofluorescence could be easily mistaken as nuclear staining. The blue "nuclear" staining in this paper is probably inaccurate since it was not verified in red or green fluorescence channels and their "nuclei"-related data might be mis-interpreted.

neuroscience↗

bioRxiv2023

Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants

The early Omicron lineage variants evolved and gave rise to diverging lineages that fueled the COVID-19 pandemic in 2022. Bivalent mRNA vaccines, designed to broaden protection against circulating and future variants, were authorized by the U.S. Food and Drug Administration (FDA) in August 2022 and recommended by the U.S. Centers for Disease Control and Prevention (CDC) in September 2022. The impact of bivalent vaccination on eliciting neutralizing antibodies against homologous BA.4/BA.5 viruses as well as emerging heterologous viruses needs to be analyzed. In this study, we analyze the neutralizing activity of sera collected after a third dose of vaccination (2-6 weeks post monovalent booster) or a fourth dose of vaccination (2-7 weeks post bivalent booster) against 10 predominant/recent Omicron lineage viruses including BA.1, BA.2, BA.5, BA.2.75, BA.2.75.2, BN.1, BQ.1, BQ.1.1, XBB, and XBB.1. The bivalent booster vaccination enhanced neutralizing antibody titers against all Omicron lineage viruses tested, including a 10-fold increase in neutralization of BQ.1 and BQ.1.1 viruses that predominated in the U.S. during the last two months of 2022. Overall, the data indicate the bivalent vaccine booster strengthens protection against Omicron lineage variants that evolved from BA.5 and BA.2 progenitors.

microbiology↗

bioRxiv2022

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

BackgroundOat (Avena sativa, 2n=6x=42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2n=6x=14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in an evolutionary context, and develop genomic resources to identify the pangenome and economic traits within Pooideae. ResultsThe 3.85 gigabase ALO genome (seven pseudo-chromosomes), contained 40,845 protein-coding genes and 87% repetitive sequences (84.21% transposable elements). An LTR retrotransposon family was abundant at all chromosome centromeres, and genes were distributed without major terminal clusters. Comparisons of synteny with A. eriantha and A. strigosa showed evolutionary translocations of terminal segments including many genes. Comparison with rice (x=12) and the ancestral grass karyotype showed synteny and features of chromosome evolution including fusions, translocations and insertions of syntenic blocks across Pooideae species. With a genome size 10 times larger than rice, ALO showed relatively uniform expansion along the chromosome arms, with few gene-poor regions along arms, and no major duplications nor deletions. Linked gene networks were identified (mixed-linkage glucans and cellulose synthase genes), and CYP450 genes may be related to salt-tolerance. ConclusionsThe high-continuity genome assembly shows gene, chromosomal structural and copy number variation, providing a reference for the Avena pangenome, defining the full spectrum of diversity. Chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.

genomics↗