Search bioRxiv⌕ Search

Biology subjects

Ding, P.

Publications and source records attributed to Ding, P..

At least 19 recordsLinked to original sources

Species diversity increases information flow about predation in bird communities

The Biodiversity-Ecosystem Functioning (BEF) literature has shown species diversity to be essential for ecosystem functioning and services. Yet although acquiring information through interspecific networks can impact ecosystem functioning, it is unclear how it is modulated by species diversity. Eliciting vocal responses using predator models across a latitudinal gradient, we first show that the species diversity of birds increases public information about predation both in the low-cost system of mobbing and in the higher-cost system of alarm calls. A similar result was also found across a fragment area gradient for mobbing; this system was then used to test how species diversity affects interspecific information flow in mobbing communities. We set up two BEF playback experiments, manipulating the species richness level of the playback sound files by varying the number of species producing mobbing calls (one, two, four, eight species). In an experiment in which the call rate across treatments was held constant, and only heterospecific responses were counted, increasing species richness of the sound files increased the number of species and individuals responding, the number of calls produced and their frequency range, and decreased latency to call. An experiment in which call rate increased with the addition of species in each treatment showed a similar, but stronger pattern. There was little evidence that the signals of one particular species changed responses. This supports the hypothesis that the species diversity of a community is a key component influencing the quantity and quality of information flow inside it.

ecology↗

Uncoupling hypersensitive cell death response and disease resistance activated by effector-triggered immunity

Effector-triggered immunity (ETI) is a major defence strategy in plants and is frequently associated with the hypersensitive response (HR), a localized form of programmed cell death long assumed to be essential for pathogen resistance. However, the causal relationship between HR and effective immunity remains unresolved. We show that the Arabidopsis cbp60g sard1 double mutant exhibits exaggerated ETI-associated HR but only partial resistance to bacterial and oomycete pathogens, thereby genetically uncoupling cell death from disease resistance without pleiotropic defects. Genome-wide transcriptome profiling reveals that the absence of CBP60g and SARD1 disrupts the balance between immune activators and suppressors, including reduced induction of the Nudix hydrolase NUDT7. Overexpression of NUDT7 diminishes but does not abolish the heightened HR phenotype in cbp60g sard1 mutant, indicating that multiple negative regulators act redundantly to restrain immune-associated cell death. These findings demonstrate that HR is not an obligatory determinant of effective resistance and provide mechanistic insight into how plants coordinate transcriptional networks to balance pathogen defence with the containment of host cell death. By refining the relationship between HR and immunity, this work challenges a long-standing paradigm in plant biology and advances our understanding of immune regulation.

plant biology↗

Cell-type-specific execution of effector-triggered immunity

Effector-triggered immunity (ETI) is a central component of host defense, but whether all cell types execute ETI similarly remains unknown. We combined chemically imposed immune activation with single-cell transcriptomics to profile ETI responses across all leaf cell types in Arabidopsis. Despite uniform ETI perception, we find striking divergence between transcriptional outputs: a core set of defense genes is broadly induced, while distinct cell types activate specialized immune modules. We infer that downstream immune execution is shaped not only by immune receptor activation, but also by cell identity and its associated transcriptional regulatory context, including local transcription factor availability and chromatin accessibility. We further demonstrate that transcriptional regulators preferentially induced in epidermal cells are required to restrict invasion by non-adapted pathogens. Their absence permits pathogen entry into deeper tissues despite intact recognition, revealing a spatial division of immune functions. Our findings uncover a layered immune architecture in plants, challenges the assumption of uniform immune execution, and provides a framework for exploring cell-type-specific resistance logic in multicellular hosts.

plant biology↗

deepTFBS: Improving within- and cross-species prediction of transcription factor binding using deep multi-task and transfer learning

The precise prediction of transcription factor binding sites (TFBSs) is crucial in understanding gene regulation. In this study, we present deepTFBS, a comprehensive deep learning (DL) framework that builds a robust DNA language model of TF binding grammar for accurately predicting TFBSs within and across plant species. Taking advantages of multi-task DL and transfer learning, deepTFBS is capable of leveraging the knowledge learned from large-scale TF binding profiles to enhance the prediction of TFBSs under small-sample training and cross-species prediction tasks. When tested using available information on 359 Arabidopsis TFs, deepTFBS outperformed previously described prediction strategies, including position weight matrix, deepSEA and DanQ, with a 244.49%, 49.15%, and 23.32% improvement of the area under the precision-recall curve (PRAUC), respectively. Further cross-species prediction of TFBS in wheat showed that deepTFBS yielded a significant PRAUC improvement of 30.6% over these three baseline models. deepTFBS can also utilize information from gene conservation and binding motifs, enabling efficient TFBS prediction in species where experimental data availability is limited. A case study, focusing on the WUSCHEL (WUS) transcription factor, illustrated the potential use of deepTFBS in cross-species applications, in our example between Arabidopsis and wheat. deepTFBS is publically available at https://github.com/cma2015/deepTFBS. One sentence summaryThe high-performing deep learning framework deepTFBS can flexibly perform within- and cross-species prediction of TF binding, transferring the transcription regulation from model to non-model species.

bioinformatics↗

Enhancing plant broad-spectrum resistance through engineered pattern recognition receptors

Conventional plant resistance breeding has primarily focused on intracellular immune receptors, while cell-surface pattern recognition receptors (PRRs) have been underexplored due to their comparatively modest contributions to resistance. However, PRRs offer significant untapped potential for crop improvement. In this study, we demonstrate that the Arabidopsis receptor-like protein RLP23, which recognizes molecular patterns from three distinct microbial kingdoms, confers broad-spectrum resistance when introduced into the Solanaceae crop tomato. We also identify the intracellular (IC) domain of RLP23 as crucial for ensuring compatibility and efficacy during heterologous expression. Targeted engineering of the IC domain significantly enhances RLP23 potential utility, enabling transfer of robust resistance against bacterial, fungal, and oomycete pathogens to other plants without compromising yield. We extended this RLP engineering strategy to rice and poplar, highlighting its broad applicability. These findings establish a versatile framework for PRR-based engineering, opening new avenues for sustainable crop protection.

plant biology↗

ABA-induced MYB transcriptional module regulates the differentiation trajectory of chickpea exodermis

Abscisic acid (ABA) regulates plant responses to stress and influences the differentiation of root barrier cell types, such as the endodermis and exodermis. Despite the importance of the exodermis in limiting water and solute fluxes, its regulation remains poorly understood in legumes. Here, we characterize the ABA-induced suberization and lignification of root tissues across eight galegoid legumes to identify exodermis-forming species in the clade. Chickpea deposited suberin lamella specifically in the outermost cortex and formed a functional apoplastic barrier, i.e. an exodermis. Transcriptomics of chickpea roots revealed ABA-induced programs that were temporally separated, specifically, a rapid program with the general ABA response, and a delayed programs of suberin and lignin biosynthesis. We identified WRKY and MYB transcription factors that putatively link the ABA response to the suberin biosynthesis, and using single-cell RNA-seq of chickpea roots we inferred an exodermis-expressed WRKY-MYB regulatory unit upstream of the suberin biosynthetic genes. Transactivation assays supported an ABA-dependent transcription factor activity upstream of suberin biosynthesis pathway in chickpea. Our results reveal a cell-type specific transcription factor hierarchy that coordinates hormone perception into an important mechanism of root plasticity in legumes.

plant biology↗

The m6A Reader ECT1 Mediates Seed Germination via the DAG2-ECT1-PHYB Regulatory Cascade in Arabidopsis

The N6-methyladenosine (m6A) RNA modification, a significant epitranscriptomic mark, is integral to plant growth and development. m6A reader proteins are capable of recognizing m6A modifications to impact RNA metabolic and biological processes. Here, we discovered ECT1 as an m6A reader protein that directly binds to the m6A site and plays a role in positively regulating seed germination in the context of gibberellins (GAs). ECT1 undergoes m6A modification to ensure its own stability and engages in self-interaction to enhance its protein stability. Moreover, ECT1 establishes a regulatory circuit with DAG2, which has been reported to play a positive regulatory role in GA-mediated seed germination. We found that DAG2 directly binds to the ECT1 promoter to control its transcription. ECT1 modulates the mRNA stability of DAG2. Furthermore, we identified PHYB, which encodes a key photoreceptor controlling GA-regulated seed germination, as a common downstream target of DAG2 and ECT1. DAG2 and ECT1 regulate the expression of PHYB at the transcriptional and post-transcriptional levels, respectively. ECT1 binds directly to PHYB, thereby influencing its stability. While DAG2 binds to the PHYB promoter to regulate its transcription. Together, these results unveil that ECT1 participates in the m6A signaling pathway through complex and multifaceted molecular mechanisms, broadening the spectrum of m6A reader functions and deepening our insight into the m6A signaling network in Arabidopsis.

plant biology↗

Habitat fragmentation mediates the mechanisms underlying long-term climate-driven thermophilization in birds

Climatic warming can shift community composition driven by the colonization-extinction dynamics of species with different thermal preferences; but simultaneously, habitat fragmentation can mediate species responses to warming. As this potential interactive effect has proven difficult to test empirically, we collected data on birds over 10 years of climate warming in a reservoir subtropical island system that was formed 65 years ago. We investigated how the mechanisms underlying climate-driven directional change in community composition were mediated by habitat fragmentation. We found thermophilization driven by increasing warm-adapted species and decreasing cold-adapted species in terms of trends in colonization rate, extinction rate, occupancy rate and population size. Critically, colonization rates of warm-adapted species increased faster temporally on smaller or less isolated islands; cold-adapted species generally were lost more quickly temporally on closer islands. This provides support for dispersal limitation and microclimate buffering as primary proxies by which habitat fragmentation mediates species range shift. Overall, this study advances our understanding of biodiversity responses to interacting global change drivers.

ecology↗

Modular mechanisms of immune priming and growth inhibition mediated by plant effector-triggered immunity

Excessive activation of effector-triggered immunity (ETI) in plants inhibits plant growth and activates cell death. ETI mediated by intracellular Toll/Interleukin-1 receptor/Resistance protein (TIR) nucleotide-binding leucine-rich-repeat receptors (NLRs) involves two partially redundant signalling nodes in Arabidopsis, EDS1-PAD4-ADR1 and EDS1-SAG101-NRG1. Genetic and transcriptomic analyses show that EDS1-PAD4-ADR1 primarily enhances the immune component abundance and is critical for limiting pathogen growth, whereas EDS1-SAG101-NRG1 mainly activates the hypersensitive cell death response (HR) but is dispensable for immune priming. This study enhances our understanding of the distinct contributions of these two signalling modules to ETI and suggests potential strategies for improving disease resistance in crops without compromising yield.

plant biology↗

Implantable nanophotonic neural probes for integrated patterned photostimulation and electrophysiology recording

Optogenetics has transformed neuroscience by allowing precise manipulation of neural circuits with light [1-5]. However, a central difficulty has been to deliver spatially shaped light and record deep within the brain without causing damage or significant heating. Current approaches form the light beam in free space and record the neural activity using fluorescence imaging or separately inserted electrodes [6-9], but attenuation limits optical penetration to around 1 mm of the brain surface [10]. Here, we overcome this challenge with foundry-fabricated implantable silicon neural probes that combine microelectrodes for electrophysiology recordings with nanophotonic circuits that emit light with engineered beam profiles and minimal thermal impact. Our experiments reveal that planar light sheets, emitted by our neural probes, excited more neurons and induced greater firing rate fatigue in layers V and VI of the motor and somatosensory cortex of Thy1-ChR2 mice at lower output intensities than low divergence beams. In the hippocampus of an epilepsy mouse model, we induced seizures, a network-wide response, with light sheets without exceeding the[~] 1{whitebullet}C limit for thermally induced electrophysiological responses [11-13]. These findings show that optical spatial profiles can be tailored for optogenetic stimulation paradigms and that the probes can photostimulate and record neural activity at single or population levels while minimizing thermal damage to brain tissue. The neural probes, made in a commercial silicon photonics foundry on 200-mm silicon wafers, demonstrate the manufacturability of the technology. The prospect of monolithically integrating additional well-established silicon photonics devices, such as wavelength and polarization multiplexers, temperature sensors, and optical power monitors, into the probes holds the potential of realizing more versatile, implantable tools for multimodal brain activity mapping.

bioengineering↗

Cell type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

Plant infection by microbial pathogens is a dynamic process. Here, we investigated the heterogeneity of plant responses in the context of pathogen location. A single-cell atlas of Arabidopsis thaliana leaves challenged by the fungus Colletotrichum higginsianum revealed cell type-specific gene expression that highlights an enrichment of intracellular immune receptors in vasculature cells. Using trajectory inference, we assigned cells that directly interacted with the invasive hyphae. Further analysis of cells at these infection sites revealed transcriptional plasticity based on cell type. A reprogramming of abscisic acid signalling was specifically activated in guard cells. Consistently, a contact-dependent stomatal closure was observed, possibly representing a defense response that anticipates pathogen invasive growth. We defined cell type-specific deployments of genes activating indole glucosinolate biosynthesis at the infection sites, and determined their contribution to resistance. This research highlights the spatial dynamics of plant response during infection and reveals cell type-specific processes and gene functions.

plant biology↗

Multi-omics analyses of single cell-derived colorectal cancer organoids reveal intratumor heterogeneity and immune response diversity

Colorectal cancer (CRC) organoids have similar genomic and functional characteristics to the original specimens. They have become a novel and promising tumor model. However, systematic research of heterogeneity and evolution based on tumor organoids and unbiased evaluation of CD4+ T cell-mediated tumor recognition is presently lacking. Here, we study the variability in genomic characterization and single-cell transcriptome between different tumor organoid clones derived from the same CRC patient. While clone-specific differences in driver gene mutations and cancer stem cell (CSC) subpopulations were observed, inter-clone heterogeneity was even more prevalent. Using single-cell RNA sequencing, we found that compared with bulk organoids, CRC organoid clones are mainly composed of cancer stem cells and transiently-amplifying cells (TACs), but no epithelial-mesenchymal transition (EMT)-like (S100A4+CDH1-) cells. In addition, we study the phenotypic characteristics and TCR properties of tumor-reactive CD4+ T cells by coupling the organoid-TILs co-culture model, single-cell profiling, and recognition testing of candidate TCRs. We found that the proliferating CD4+ T cells increased significantly from 7.1% to 35.4%, and the TCR clonotypes increased from 110 to 1043 after co-culture with organoids. Moreover, 4 of 10 (40%) candidate TCRs with a significant increase in clone abundance exhibited tumor recognition. These results provide evidence that the proliferating CD4+ T cells with clonal expansion after co-culture with tumor organoids are the potential tumor-reactive T cells. Collectively, we reconstructed intra-patient heterogeneity in single cell-derived organoid models and characterized the phenotypic characteristics and functional properties of tumor-reactive CD4+ T cells.

cancer biology↗

Osteocytes regulate organismal senescence of bone and bone marrow

The skeletal system contains a series of sophisticated cellular lineages arisen from the mesenchymal stem cells (MSC) and hematopoietic stem cells (HSC), that determine the homeostasis of bone and bone marrow. Here we reasoned that osteocyte may exert a function in regulation of these lineage cell specifications and tissue homeostasis. Using a mouse model of conditional deletion of osteocytes by the expression of diphtheria toxin subunit (DTA) in dentin matrix protein 1 (DMP-1) positive osteocytes, we demonstrated that partial ablation of DMP-1positive osteocytes caused severe sarcopenia, osteoporosis and degenerative kyphosis, leading to shorter lifespan in these animals. Osteocyte reduction altered mesenchymal lineage commitment resulting in impairment of osteogenesis and induction of osteoclastogensis. Single cell RNA sequencing further revealed that hematopoietic lineage was mobilized towards myeloid lineage differentiation with expanded myeloid progenitors, neutrophils and monocytes, while the lymphopoiesis was impaired with reduced B cells in the osteocyte ablation mice. The acquisition of a senescence-associated secretory phenotype (SASP) in both osteoprogenic and myeloid lineage cells was the underlying cause. Together, we showed that osteocytes play critical roles in regulating of lineage cell specifications in bone and bone marrow through mediation of organismal senescence.

cell biology↗

Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin

Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.

bioinformatics↗

Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing

BackgroundImmune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited. MethodsIn this study, we compared the single-cell transcriptomes of 77{square}957 immune cells from 12 species using single-cell RNA-sequencing (scRNA-seq). Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells. ResultsResults revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular crosstalk and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM-CD44 was highly conserved among the immune cells. ConclusionsThis study is the first to provide a comprehensive analysis of the cross-species single-cell atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders.

cell biology↗

Screening of cell-virus, cell-cell, gene-gene interactions among kingdoms of life at single cell resolution

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) issued a significant and urgent threat to global health. The exact animal origin of SARS-CoV-2 remains obscure and understanding its host range is vital for preventing interspecies transmission. Previously, we have assessed the target cell profiles of SARS-CoV-2 in pets, livestock, poultry and wild animals. Herein, we expand this investigation to a wider range of animal species and viruses to provide a comprehensive source for large-scale screening of potential virus hosts. Single cell atlas for several mammalian species (alpaca, hamster, hedgehog, chinchilla etc.), as well as comparative atlas for lung, brain and peripheral blood mononuclear cells (PBMC) for various lineages of animals were constructed, from which we systemically analyzed the virus entry factors for 113 viruses over 20 species from mammalians, birds, reptiles, amphibians and invertebrates. Conserved cellular connectomes and regulomes were also identified, revealing the fundamental cell-cell and gene-gene cross-talks between these species. Overall, our study could help identify the potential host range and tissue tropism of SARS-CoV-2 and a diverse set of viruses and reveal the host-virus co-evolution footprints.

cell biology↗

Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor.

Plants use intracellular immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. We report here the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY. Perception of AvrRps4C by RRS1WRKY is mediated by the {beta}2-{beta}3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C. Structure-based mutations that disrupt AvrRps4C/RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA binding domain of AtWRKY41, with similar binding affinities. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity. SignificanceThis study reveals a mechanism of effector recognition by a plant NLR immune receptor that carries an integrated domain (ID) which mimics an authentic pathogen effector target. An Arabidopsis immune receptor carrying RRS1 and RPS4 NLR proteins detects the Pseudomonas syringae pv. pisi secreted effector AvrRps4 via a WRKY ID in RRS1. We used structural biology to reveal the mechanisms of AvrRps4/WRKY interaction and demonstrated that this binding is essential for effector recognition in planta. Our analysis revealed distinctive features of the WRKY ID that mediate the recognition of structurally distinct effectors from different bacterial pathogens. These insights could enable engineering NLRs with novel recognition specificities, and enhances our understanding of how effectors interact with host proteins.

plant biology↗

Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics

Civets are small mammals belonging to the family Viverridae. The masked palm civets (Paguma larvata) served as an intermediate host in the bat-to-human transmission of severe acute respiratory syndrome coronavirus (SARS-CoV) in 20031. Because of their unique role in the SARS outbreak, civets were suspected as a potential intermediate host of SARS-CoV-2, the etiological pathogen of the COVID-19 pandemic. Besides their susceptibility to coronaviruses, civets can also be infected by other viruses, such as canine distemper viruses2, parvoviruses3, influenza viruses4, etc. Regarding the ecological and economical role of civets, it is vital to evaluate the potential threats from different pathogens to these animals. Receptor binding is a necessary step for virus entry into host cells. Understanding the distribution of receptors of various viruses provides hints to their potential tissue tropisms. Herein, we characterized the cell atlas of five important organs (the frontal lobe, lung, liver, spleen and kidney) of masked palm civets (Paguma larvata) and described the expression profiles of receptor associated genes of 132 viruses from 25 families, including 16 viruses from 10 families reported before that can attack civets and 116 viruses with little infection record.

immunology↗