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Dong, B.

Publications and source records attributed to Dong, B..

At least 37 records · Page 2Linked to original sources

Real-Time and Site-Specific Perturbation of Dynamic Subcellular Compartments Using Femtosecond Pulses

Understanding laser interactions with subcellular compartments is crucial for advancing optical microscopy, phototherapy, and optogenetics. While continuous-wave (CW) lasers rely on linear absorption, femtosecond (fs) lasers enable nonlinear multiphoton absorption confined to the laser focus, offering high axial precision. However, current fs laser delivery methods lack the ability to target dynamic molecular entities and automate target selection, limiting real-time perturbation of biomolecules with mobility or complex distribution. Additionally, existing technologies separate fs pulse delivery and imaging, preventing simultaneous recording of cellular responses. To overcome these challenges, we introduce fs real-time precision opto-control (fs-RPOC), which integrates a laser scanning microscope with a closed-loop feedback mechanism for automated, chemically selective subcellular perturbation. fs-RPOC achieves superior spatial precision and fast response time, enabling single- and sub-organelle microsurgery of dynamic targets and localized molecular modulation. By applying a pulse-picking method, fs-RPOC independently controls laser average and peak power at any desired subcellular compartment. Targeting mitochondria, fs-RPOC reveals site-specific molecular responses resulting from fs-laser-induced ROS formation, H2O2 diffusion, and low-density plasma generation. These findings offer new insights into fs laser interactions with subcellular compartments and demonstrate fs-RPOCs potential for precise molecular and organelle regulation.

bioengineering↗

Integrative Omics reveals genetic basis and TaMYB7-A1's function in wheat WUE and drought resilience

Improving water use efficiency (WUE) and drought resistance in wheat is critical for ensuring global food security under changing climate conditions. Here, we integrated multi-omic data, including population-scale phenotyping, transcriptomics, and genomics, to dissect the genetic and molecular mechanisms underlying WUE and drought resilience in wheat. Genome-wide association studies (GWAS) revealed 8,135 SNPs associated with WUE-related traits, identifying 258 conditional and non-conditional QTLs, many of which co-localized with known drought-resistance genes. Pan-transcriptome analysis uncovered tissue-specific expression patterns, core and unique gene functions, and dynamic sub-genomic biases in response to drought. eQTL mapping pinpointed 146,966 regulatory loci, including condition-specific hotspots enriched for genes involved in water regulation, osmoregulation, and photosynthesis. Integration of Weighted gene co-expression network analysis (WGCNA), Summary-data-based Mendelian Randomization (SMR) and GWAS, eQTLs identified 207 candidate causal genes as key regulators for WUE-related traits in wheat, such as TaMYB7-A1. Functional analyses found that TaMYB7-A1 enhances drought tolerance by promoting root growth, reducing oxidative stress, and improving osmotic regulation, enabling better water access and survival under stress. It also increases photosynthesis efficiency and WUE, boosting yield under drought without compromising performance in well-watered conditions, making it ideal target for breeding. Our findings provide a comprehensive omic framework for understanding the genetic architecture of WUE and drought resistance, offering valuable targets for breeding resilient wheat varieties.

plant biology↗

All ribosomal RNAs and 45S spacers from humans to worms are packed with organism-specific motifs whose other copies are found predominantly in numerous nervous system genes including many associated with human disorders

The nucleotide sequences of ribosomal RNAs (rRNAs) and the spacers of 45S are tuned to fulfill optimally their respective roles during ribosome biosynthesis and function. We report that these sequences satisfy additional genome-wide constraints in humans, mice, fruit flies, and worms. In all four organisms, the rRNAs and 45S spacers are densely packed with organism-specific nucleotide motifs with many additional identical copies throughout the genome. The human rRNAs and 45S spacers contain 1,723 motifs whose sequences are unique to the rRNAs/spacers of primates. These motifs have numerous additional exact intronic and exonic copies whose genomic placement is also unique to primates. Specific combinations of the motifs appear exclusively in 3,430 human nervous system and developmental genes, including 1,046 risk genes for autism, schizophrenia, and bipolar disorder. RNA/RNA crosslinking experiments show that the rRNA/spacer motifs are contact points for rRNA-mRNA and mRNA-mRNA heteroduplexes. RNA binding protein (RBP) assays show that these motifs are also in the binding sites of 113 RBPs. RNA sequencing reveals that rRNAs and spacers produce endogenous small non-coding RNAs (sncRNAs) that carry the same primate-specific motifs. Lastly, the motifs intergenic and intronic copies overlap 131 GWAS polymorphisms associated with neuropathologies (p-val<3.9e-12). The findings suggest that the motifs facilitate RNA/RNA and RBP/RNA interactions that are affected by polymorphisms and modulated by rRNA- and spacer-derived sncRNAs carrying the same motifs. Our study also genetically links for the first time rRNAs and 45S spacers to autism and other typically human neurological disorders. Mutation panels based on these motifs can lead to new molecular diagnostics for these disorders, whereas snRNAs carrying these motifs can serve as drugs or potential therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/627812v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@146feadorg.highwire.dtl.DTLVardef@1fa501corg.highwire.dtl.DTLVardef@a17f14org.highwire.dtl.DTLVardef@9e2053_HPS_FORMAT_FIGEXP M_FIG C_FIG The human ribosomal RNAs and the 45S spacers share primate-specific motifs with thousands of nervous system genes, including risk genes for autism and other neurological disorders. Similar links between rRNAs/spacers and nervous system genes exist in mice, fruit flies, and worms but are achieved through motifs that are unique to each organism. In humans, the motifs are at the contact points of endogenous gene-gene and rRNA-gene heteroduplexes, as well as the binding sites of RNA binding proteins (RBPs) in genes and rRNAs/spacers. Endogenous small RNAs carrying these shared motifs modulate these endogenous interactions and are disrupted by mutations at the motifs genomic copies. Mutation panels based on these motifs can lead to new diagnostics for autism and other disorders, while the small RNAs carrying the motifs can serve as drugs or potential therapeutic targets.

neuroscience↗

Versatile Stain Transfer in Histopathology Using a Unified Diffusion Framework

Histological staining is vital in clinical pathology for visualizing tissue structures. However, these techniques are laborious and time-consuming. Digital virtual staining offers a promising solution, but existing methods typically rely on Generative Adversarial Networks (GANs), which may suffer from artifacts and mode collapse. Motivated by the success of diffusion models, we present DUST, a novel Diffusion-based Unified framework for versatile Stain Transfer in histopathology. To enhance domain awareness and task-specific performance, we propose a dual encoding strategy that integrates the stain types of both the source and target domains. Additionally, we introduce a dynamic dual-output head to address the unstable intensity issue encountered with conventional DDPM implementations. Validated on a curated fourstain kidney histopathological dataset (H&E, MT, PAS, and PASM), DUST demonstrates superior versatile stain transfer capabilities. Our research highlights the potential of diffusion models to advance virtual staining, paving the way for more efficient digital pathology analyses.

pathology↗

AmygdalaGo-BOLT3D: A boundary learning transformer for tracing human amygdala

Each year, thousands of brain MRI scans are collected to study structural development in children and adolescents. However, the amygdala, a particularly small and complex structure, remains difficult to segment reliably, especially in developing populations where its volume is even smaller. To address this challenge, we developed AmygdalaGo-BOLT, a boundary-aware deep learning model tailored for human amygdala segmentation. It was trained and validated using 854 manually labeled scans from pediatric datasets, with independent samples used to ensure performance generalizability. The model integrates multiscale image features, spatial priors, and self-attention mechanisms within a compact encoder-decoder architecture to enhance boundary detection. Validation across multiple imaging centers and age groups shows that AmygdalaGo-BOLT closely matches expert manual labels, improves processing efficiency, and outperforms existing tools in accuracy. This enables robust and scalable analysis of amygdala morphology in developmental neuroimaging studies where manual tracing is impractical. To support open and reproducible science, we publicly release both the labeled datasets and the full source code. TeaserAn AI model enables accurate amygdala segmentation across ages and centers, supporting large-scale brain imaging studies.

neuroscience↗

The Neuropeptide Sulfakinin, a peripheral regulator of insect behavior switch between mating and foraging

Behavioral strategies for foraging and reproduction in the oriental fruit fly (Bactrocera dorsalis) are alternative options for resource allocation and are controlled by neuropeptides. Here we show that the behavioral switch between foraging and reproduction is associated with changes in antennal sensitivity. Starved flies became more sensitive to food odors while suppressing their response to opposite-sex pheromones. The gene encoding sulfakinin receptor 1 (SkR1) was significantly upregulated in the antennae of starved flies, so we tested the behavioral phenotypes of null mutants for the genes encoding the receptor (skr1-/-) and its ligand sulfakinin (sk-/-). In both knockout lines, the antennal responses shifted to mating mode even when flies were starved. This suggests that sulfakinin signaling via SkR1 promotes foraging while suppressing mating. Further analysis of the mutant flies revealed that sets of odorant receptor (OR) genes were differentially expressed. Functional characterization of the differentially expressed ORs suggested that sulfakinin directly suppresses the expression of ORs that respond to opposite-sex hormones while enhancing the expression of ORs that detect food volatiles. We conclude that sulfakinin signaling via SkR1, modulating OR expressions and leading to altered antenna sensitivities, is an important component in starvation-dependent behavioral change.

ecology↗

TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat

Cultivating high-yield wheat under limited water resources is essential for sustainable agriculture in semiarid regions. Amid water scarcity, plants activate drought response signaling, yet the delicate balance between drought tolerance and development remains unclear. Through genome-wide-association study (GWAS) and transcriptome profiling, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor (TF), TabHLH27-A1, as a promising quantitative trait locus (QTL) candidate for both relative root dry weight (DW.R%) and spikelet number per spike (SPS) in wheat. TabHLH27-A1/B1/D1 knockout reduced wheat drought tolerance, yield, and water use efficiency (WUE). TabHLH27-A1 exhibited rapid induction with PEG treatment, gradually declining over days. It activated stress response genes such as TaCBL8-B1 and TaCPI2-A1 while inhibiting root growth genes like TaSH15-B1 and TaWRKY70-B1 under short-term PEG stimulus. The distinct transcriptional regulation of TabHLH27-A1 involved diverse interacting factors such as TaABI3-D1 and TabZIP62-D1. Natural variations of TabHLH27-A1 influences its transcriptional responses to drought stress, with TabHLH27-A1Hap-II associated with stronger drought tolerance, larger root system, more spikelets, and higher WUE in wheat. Significantly, the elite TabHLH27-A1Hap-II was selected during the breeding process in China, and introgression of TabHLH27-A1Hap-II allele improves drought tolerance and grain yield, especially under water-limited conditions. Our study highlights TabHLH27-A1s role in balancing root growth and drought tolerance, providing a genetic manipulation locus for enhancing WUE in wheat.

genetics↗

Unleashing precision and freedom of optical manipulation: Software-aided real-time precision opto-control of intracellular molecular activities and cell functions

The traditional method in biological science to regulate cell functions often employs chemical interventions, which commonly lack precision in space and time. While optical manipulation offers superior spatial precision, existing technologies are constrained by limitations in flexibility, accuracy, and response time. Here, we present an adaptable and interactive optical manipulation platform that integrates laser scanning, chemical sensing, synchronized multi-laser control, adaptable target selection, flexible decision-making, and real-time monitoring of sample responses. This software-assisted real-time precision opto-control (S-RPOC) platform facilitates automatic target selection driven by optical signals while permitting user-defined manual delineation. It allows the treatment of mobile or stationary targets with varying laser dosages and wavelengths simultaneously at diffraction-limited spatial precision and optimal accuracy. Significantly, S-RPOC showcases versatile capabilities including adaptive photobleaching, comprehensive quantification of protein dynamics, selective organelle perturbation, control of cell division, and manipulation of individual cell behaviors within a population. With its unprecedented spatiotemporal precision and adaptable decision-making, S-RPOC holds the potential for extensive applications in biological science.

cell biology↗

Spectrally Resolved Localization Microscopy with Ultrahigh-Throughput

Single-molecule localization microscopy (SMLM) has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features quickly and accurately in complex environments at the nanoscopic level. Multicolor super-resolution imaging has seen the greatest advancement among SMLM techniques, drastically improving the differentiation ability of nanostructures beyond the diffraction limit and increasing the resolution with which previously unresolvable structures are studied. However, current multicolor SMLM methodologies present low spatial resolution and throughput and require complex optical systems. Here, we overcome these drawbacks by developing an ultrahigh-throughput SMLM methodology that allows for ultrahigh throughput multicolor imaging at the nanoscopic level using a color glass filter. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5nm spectral precisions.

biophysics↗

Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization

Being able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late-stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early-stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real-time precision opto-control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito-Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions. TeaserMicrotubule dynamics in live cells allow quantification of cellular phototoxicity of fluorescent dyes in various conditions

cell biology↗

Extracellular Matrix Abnormalities Contribute to Cardiac Insulin Resistance and Associated Dysfunction in Diet-induced Obese Mice

Increased deposition of extracellular matrix (ECM) components such as collagens and hyaluronan contributes to the pathogenesis of obesity-associated insulin resistance in muscle, liver, and adipose tissue. Despite the significance of the heart in cardiovascular and metabolic diseases, maladaptive ECM remodelling in obesity-associated cardiac insulin resistance and cardiac dysfunction has not been studied. Using genetic and pharmacological approaches in mice fed a high fat (HF) diet, we demonstrated a tight association between increased ECM deposition with cardiac insulin resistance. Increased collagen deposition by genetic deletion of matrix metalloproteinase 9 (MMP9) exacerbated cardiac insulin resistance and decreased hyaluronan deposition by treatment with PEGylated human recombinant hyaluronidase PH20 (PEGPH20) improved cardiac insulin resistance in obese mice. These relationships corresponded to functional changes in the heart. PEGPH20 treatment in obese mice ameliorated HF diet-induced abnormal myocardial remodelling. In addition to hyaluronan, increased collagen deposition is a characteristic of the obese mouse heart. We further demonstrated that pirfenidone, a clinically available anti-fibrotic medication which inhibits collagen expression, improved cardiac insulin resistance and cardiac function in obese mice. Our results provide important new insights into the role of ECM remodelling in the pathogenesis of cardiac insulin resistance and associated dysfunction in obesity of distinct mouse models. These findings support the novel therapeutic potential of targeting early cardiac ECM abnormalities in the prevention and treatment of obesity-related cardiovascular complications.

physiology↗

IL-33-binding HpARI family homologues with divergent effects in suppressing or enhancing Type 2 immune responses

HpARI is an immunomodulatory protein secreted by the intestinal nematode Heligmosomoides polygyrus bakeri, which binds and blocks IL-33. Here, we find that the H. polygyrus bakeri genome contains 3 HpARI family members, and that these have different effects on IL-33-dependent responses in vitro and in vivo, with HpARI1+2 suppressing, and HpARI3 amplifying these responses. All HpARIs have sub-nanomolar affinity for mouse IL-33, however HpARI3 does not block IL-33-ST2 interactions. Instead, HpARI3 stabilises IL-33, increasing the half-life of the cytokine and amplifying responses to it in vivo. Together these data show that H. polygyrus bakeri secretes a family of HpARI proteins with both overlapping and distinct functions, comprising a complex immunomodulatory arsenal of host-targeted proteins.

immunology↗

Kin selection as a modulator of human handedness: sex-specific, parental and parent-of-origin effects

The frequency of left-handedness in humans is [~]10% worldwide and slightly higher in males than females. Twin and family studies estimate the heritability of human handedness at around 25%. The low but substantial frequency of left-handedness has been suggested to imply negative frequency-dependent selection, e.g. owing to a "surprise" advantage of left-handers in combat against opponents more used to fighting right-handers. Because such game-theoretic hypotheses involve social interaction, here, we perform an analysis of the evolution of handedness based on kin-selection, which is understood to play a major role in the evolution of social behaviour generally. We show that: (1) relatedness modulates the balance of right-handedness versus left-handedness, according to whether left- handedness is marginally selfish versus marginally altruistic; (2) sex differences in relatedness to social partners may drive sex differences in handedness; (3) differential relatedness of parents and offspring may generate parent-offspring conflict and sexual conflict leading to the evolution of maternal and paternal genetic effects in relation to handedness; and (4) differential relatedness of maternal-origin versus paternal-origin genes may generate intragenomic conflict leading to the evolution of parent-of-origin-specific gene effects--such as "genomic imprinting"--and associated maladaptation.

evolutionary biology↗

Targeting pioneer transcription factor Ascl1 to promote optic nerve regeneration

In adult mammalian central nervous system (CNS) neurons, axon regeneration after injury remains limited due to unfavorable gene regulatory programs. Factors enabling comprehensive epigenetic and transcriptional transitions, for instance, pivotal transcription factors that mediate neurogenesis and morphogenesis may be sufficient to promote CNS axon regeneration. Based on the analyses of multiple public whole-genome RNA and chromatin accessibility sequencing dataset of mouse retina development, as well as previous functional studies on the regeneration-capable dorsal root ganglion neurons, we hypothesize that the overexpression of pioneer transcription factor Achaete-Scute homolog 1 (Ascl1) would promote axon regeneration in the adult mammalian CNS neurons. We employed the optic nerve crush in mice, a common model for studying CNS axon regeneration, neuron survival and glaucoma, to investigate the effect of Ascl1 overexpression on the post-injury optic nerve regeneration. We found that Ascl1 could sufficiently promote regenerated axons past the crush site and significantly preserve the survival of retinal ganglion cells. Mechanistically, we revealed that effects of Ascl1 was mediated by known pro-regeneration factor Sox11 but not others. Together, our study established an effective workflow combined with the integrated computational inference and experimental validation for discovering functionally important target for promoting CNS neuron axon regeneration and survival.

neuroscience↗

Spatiotemporal precise optical manipulation of intracellular molecular activities

Controlling chemical processes in live cells is a challenging task. The spatial heterogeneity of biochemical reactions in cells is often overlooked by conventional means of incubating cells with desired chemicals. A comprehensive understanding of spatially diverse biochemical processes requires precise control over molecular activities at the subcellular level. Herein, we develop a closed-loop optoelectronic control system that allows the manipulation of biomolecular activities in live cells at high spatiotemporal precision. Chemical-selective fluorescence signals are utilized to command lasers that trigger specific chemical reactions or control the activation of photoswitchable inhibitors at desired targets. We demonstrate the capability to selectively produce reactive oxygen species (ROS) solely at targeted organelles using blue light. Notably, the induction of ROS in the endoplasmic reticulum leads to a more pronounced disruption of tubulin polymerization and a reduction in green fluorescent protein signals, in comparison to that in lipid droplets. Moreover, when combined with a photoswitchable inhibitor, we selectively inhibit tubulin polymerization within subcellular compartments. This technology enables spatiotemporal control over chemical processes and drug activities, exclusively at desired targets, while minimizing undesired effects on non-targeted locations.

cell biology↗

Expression and molecular regulation of key genes during adipogenesis of neural crest stem cells

Neural crest stem cells (NCSCs) are pluripotent stem cells derived from the "fourth germ layer". Similar to mesenchymal stem cells (MSCs), NCSCs can differentiate into a variety of cell types, such as adipocytes. However, the mechanism of NCSCs adipogenesis remains unclear. Previously, we have revealed that primary cells have neural crest and stem cell properties and can differentiate into adipocytes. Therefore, in this study, the differentially expressed genes (DEGs) of NCSCs at specific time points of adipogenesis were predicted by mRNA sequencing, the key genes of adipogenesis were predicted by principal component analysis, heat map, GO and KEGG enrichment analysis, and the expression of DEGs was verified by RT-qPCR. RNA interference (RNAi) technology was used to inhibit the expression of DEGs, and RT-qPCR and Western blot were used to explore the regulatory mechanism between DEGs. Sequencing results indicated a possible regulatory relationship between C/EBP, C/EBP{beta}, C/EBP{delta} and PPAR{gamma}. The results of RT-qPCR were consistent with those of mRNA sequencing. Combined with RT-qPCR and western blot results, we found that C/EBP{beta} and PPAR{gamma} regulated the transcription of C/EBP during NCSCs adipogenesis, and C/EBP{beta} and PPAR{gamma} formed positive feedback loop.

developmental biology↗

Spatially-resolved single-cell atlas of ascidian endostyle provides insights into the origin of vertebrate pharyngeal organs

The pharynx is an endoderm innovation in deuterostome ancestors, the vertebrate descendent structure of which is a pharyngeal developmental organizer involving multi-germ layer and organ derivatives. However, the evolutionary origination of complicated pharynx organs in vertebrates is still largely unknown. Endostyle, a transitional pharyngeal organ exclusively in basal chordates provides an opportunity to reveal the origin of pharyngeal organs. Here, utilizing cutting-edged Stereo-seq and single-cell RNA-seq, we constructed the first spatially-resolved single-cell atlas in the endostyle of urochordate ascidian Styela clava, where the spatial location of Stereo-seq and high capture efficiency of single-cell RNA-seq complement each other and identified 23 highly differentiated cell types. We identified a previously overlooked hemolymphoid region (HLR), which harbors immune and blood cell clusters with enriched stemness capacities, illuminating a mixed rudiment and stem-cell niches for the blood and lymphoid system. More excitingly, we discovered a mechanical-sensitive hair cell candidate in zone 3 homologous to vertebrate acoustico-lateralis system, which was supported by the expression of in situ hybridization-verified inner ear-specific markers, including PTPRQ, USH2A, WHRN, and ADGRV1, ultracellular structure evidence and cross-species comparison. These results thoroughly renewed the comprehension of the basal-chordate pharynx and provides expressional evidence for multiplexed pharyngeal organ evolution.

evolutionary biology↗

Arc ubiquitination regulates endoplasmic reticulum-mediated Ca2+ release and CaMKII signaling

Synaptic plasticity relies on rapid, yet spatially precise signaling to alter synaptic strength. Arc is a brain enriched protein that is rapidly expressed during learning-related behaviors and is essential for regulating metabotropic glutamate receptor-mediated long-term depression (mGluR-LTD). We previously showed that disrupting the ubiquitination capacity of Arc enhances mGluR-LTD; however, the mechanism by which this occurs and its consequences on other mGluR-mediated signaling events is unknown. Here we show that disrupting Arc ubiquitination on key amino acid residues leads to derangements in Ca2+ release from the endoplasmic reticulum (ER) during pharmacological activation of Group I mGluRs. These alterations were observed in all neuronal subregions except secondary branchpoints. Deficits in Arc ubiquitination increased Arc self-association and enhanced its interaction with calcium/calmodulin-dependent protein kinase IIb (CaMKIIb) and constitutively active forms of CaMKII. Notably, these interactions were also excluded at secondary branchpoints. Finally, disruptions in Arc ubiquitination were found to increase Arc interaction with the integral ER protein Calnexin. These results suggest a previously unknown role for Arc ubiquitination in the fine tuning of ER-mediated Ca2+ signaling that is needed for mGluR-LTD, which in turn, may regulate CaMKII and its interactions with Arc.

neuroscience↗