Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus.

Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation.

The transcriptional landscape of Populus pattern/effector-triggered immunity and how PagWRKY18 involved in it.

Plants trigger a robust immune response by activating massive transcriptome reprogramming through crosstalk between PTI and ETI. However, how PTI and ETI contribute to the quantitative or/and qualitative output of immunity and how they work together when both are being activated were unclear. In this study, we performed a comprehensive overview of pathogen-triggered transcriptomic reprogramming by analyzing temporal changes in the transcriptome up to 144 h after Colletotrichum gloeosporioides inoculated in Populus.

High-quality maple genome reveals duplication-facilitated leaf color diversity.

Acer truncatum is a horticultural tree species with individuals that display either yellow or red leaves in autumn, giving it high ornamental and economic value. 'Lihong' of A. truncatum is an excellent cultivar due to its characteristic of having autumn leaves that turn a bright and beautiful shade of red, while its closely related cultivar 'Bunge' does not.

PPGR: a comprehensive perennial plant genomes and regulation database.

Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.

A genome-wide association study reveals that epistasis underlies the pathogenicity of .

spp. are important bacterial pathogens that cause soft rot symptoms in various crops. However, their mechanism of pathogenicity requires clarity to help control their infections.

Conserved hierarchical gene regulatory networks for drought and cold stress response in .

Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses.

Occurrence, Characteristics, and qPCR-Based Identification of Causing Soft Rot of Chinese Cabbage in China.

is one of the most important genera of phytopathogenic bacteria. It can cause soft-rot diseases on a wide range of plant species across the world. In this study, three strains (KC01, KC02, and KC03) were isolated from soft-rotted Chinese cabbage in Beijing, China.

Multifeature analysis of age-related microbiome structures reveals defense mechanisms of Populus tomentosa trees.

Root microbiota composition shifts during the development of most annual plants. Although some perennial plants can live for centuries, the host-microbiome partnerships and interaction mechanisms underlying their longevity remain unclear. To address this gap, we investigated age-related changes in the root metabolites, transcriptomes, and microbiome compositions of 1- to 35-yr-old Populus tomentosa trees.

root exudates are associated with rhizosphere microbial communities and symbiotic patterns.

Introduction: Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in rhizosphere is not well understood.

Methods: This study measured soil physiochemistry properties and root exudates in a representative forest consists of four species.

Growth-regulating factor 15-mediated gene regulatory network enhances salt tolerance in poplar.

Soil salinity is an important determinant of crop productivity and triggers salt stress response pathways in plants. The salt stress response is controlled by transcriptional regulatory networks that maintain regulatory homeostasis through combinations of transcription factor (TF)-DNA and TF-TF interactions. We investigated the transcriptome of poplar 84 K (Populus alba × Populus glandulosa) under salt stress using samples collected at 4- or 6-h intervals within 2 days of salt stress treatment.

Enantio- and diastereoselective boron conjugate addition to α-alkyl α,β-unsaturated esters.

We developed a copper-catalyzed enantio- and diastereoselective boron conjugate addition to α-alkyl α,β-unsaturated esters under base-free conditions. The approach showed excellent enantioselectivities (87-99% ee) and moderate to good conversions (51-99%), albeit with moderate diastereoselectivities (1 : 1-17 : 1 dr). The synthetic utility of this protocol was demonstrated.

Assessment of carbon emission and primary energy input of a gasoline combustion-powered 2.0 T SUV in China.

With the use of vehicles, large amounts of carbon dioxide are emitted by combustion of gasoline and energy consumes in their lifecycle. Therefore, the objective of this study is to evaluate the lifecycle carbon emission and primary energy input of a widely used sport utility vehicle (SUV) in China with the lifecycle assessment method. The results show that total petrol consumption of an SUV in lifetime is 21,300 kg; the CO emissions and primary energy input in the manufacturing, assembly, operation, and decommissioning phase are respectively 8857, 443, 54,925, and 443 kg and 123,413, 6171, 12,341, and 6171 MJ.

Machine Learning-Aided Design of Gold Core-Shell Nanocatalysts toward Enhanced and Selective Photooxygenation.

We demonstrate the use of the machine learning (ML) tools to rapidly and accurately predict the electric field as a guide for designing core-shell Au-silica nanoparticles to enhance O sensitization and selectivity of organic synthesis. Based on the feature importance analysis, obtained from a deep neural network algorithm, we found a general and linear dependent descriptor (θ ∝ , where , , and are the shape constant, size of metal nanoparticles, and distance from the metal surface) for the electric field around the core-shell plasmonic nanoparticle. Directed by the new descriptor, we synthesized gold-silica nanoparticles and validated their plasmonic intensity using scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) mapping.

Soil Layers Impact Soil Microbial Composition in the Ailao Mountains Subtropical Forest, Yunnan, China.

Plant litter decomposition is a complex, long-term process. The decomposition of litterfall is a major process influencing nutrient balance in forest soil. The soil microbiome is exceptionally diverse and is an essential regulator of litter decomposition.

Revisiting the Mg/TMSCl/Dipolar Solvent System for Dearomatic Silylation of Aryl Carbonyl Compounds: Substrate Scope, Transformations, and Mechanistic Studies.

Dearomatic silylation of arene derivatives is an intriguing synthetic target, which represents an elegant extension of Birch reduction and produces silylated cyclohexene derivatives with great potential of further transformation. Herein, we report a systematic study on dearomatic silylation of aryl carbonyl compounds with Mg and the TMSCl/NMP adduct. The protocol displays a wide range of substrate scope, including alkyl aryl ketones, aromatic amides, benzonitriles, -butyl benzoates, and even 2,2'-bipyridines.

Conductive Hydrogel Conduits with Growth Factor Gradients for Peripheral Nerve Repair in Diabetics with Non-Suture Tape.

Diabetic patients suffer from peripheral nerve injury with slow and incomplete regeneration owing to hyperglycemia and microvascular complications. This study develops a graphene-based nerve guidance conduit by incorporating natural double network hydrogel and a neurotrophic concentration gradient with non-invasive treatment for diabetics. GelMA/silk fibroin double network hydrogel plays quadruple roles for rapid setting/curing, suitable mechanical supporting, good biocompatibility, and sustainable growth factor delivery.

Bacterial Infection Induces Ultrastructural and Transcriptional Changes in the King Oyster Mushroom ().

(king oyster mushroom) is a commercially important mushroom with high nutritional and economic value. However, soft rot disease, caused by the pathogenic bacterium poses a threat to its quality and production. Morphological and ultrastructural observations of were conducted at early, middle, and late stages of infection.

Rhodium-Catalyzed Ring Expansion of Azetidines via Domino Conjugate Addition/N-Directed α-C(sp)-H Activation.

A facile synthetic method for 4-aryl-4,5-dihydropyrrole-3-carboxylates is developed, with a rhodium-catalyzed ring expansion strategy from readily available 2-(azetidin-3-ylidene) acetates and aryl boronic acids. Mechanistic investigations suggest a novel domino "conjugate addition/N-directed α-C(sp)-H activation" process. The asymmetric catalytic synthesis of the 4-aryl-4,5-dihydropyrrole-3-carboxylate is realized by using QuinoxP* (91-97% ee).

Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in .

Transposable elements (TEs) are a class of mobile genetic elements that make effects on shaping rapid phenotypic traits of adaptive significance. TE insertions are usually related to transcription changes of nearby genes, and thus may be subjected to purifying selection. Based on the available genome resources of , we found that the composition of Helitron DNA family were highly variable and could directly influence the transcription of nearby gene expression, which are involving in stress-responsive, programmed cell death, and apoptosis pathway.

Distinct and Overlapping Functions of MYB Transcription Factors SCM1 and MYB103 in Lignin Biosynthesis.

Cell wall recalcitrance is a major constraint for the exploitation of lignocellulosic biomass as a renewable resource for energy and bio-based products. Transcriptional regulators of the lignin biosynthetic pathway represent promising targets for tailoring lignin content and composition in plant secondary cell walls. However, knowledge about the transcriptional regulation of lignin biosynthesis in lignocellulosic feedstocks, such as Miscanthus, is limited.

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool.

Drought is a major threat to crop productivity and causes decreased plant growth, poor yields, and crop failure. Nevertheless, the frequency of droughts is expected to increase in the coming decades. The microbial communities associated with crop plants can influence how plants respond to various stresses; hence, microbiome manipulation is fast becoming an effective strategy for improving the stress tolerance of plants.

Comprehensive Genomic Analysis of the Endophytic Strain GLB197, a Potential Biocontrol Agent of Grape Downy Mildew.

has been extensively studied for agricultural application as a biocontrol agent. GLB197, an endophytic bacterium isolated from grape leaves, exhibits distinctive inhibition to grape downy mildew based on unknown mechanisms. To determine the genetic traits involved in the mechanism of biocontrol and host-interaction traits, the genome sequence of GLB197 was obtained and further analyzed.

Aqueous Protein-Polymer Bioconjugation via Photoinduced RAFT Polymerization Using High Loading Heterogeneous Catalyst.

Light-driven polymerization, such as photoinduced electron/energy transfer-reversible addition-fragmentation chain transfer (PET-RAFT) polymerization, enables biological benign conditions and versatile functional polymer structure design, which is readily used in protein-polymer bioconjugates. However, conventional metalloporphyrinic homogeneous catalysts for PET-RAFT polymerization suffer from limited aqueous solubility and tedious purification. Here we demonstrate the design of PET-RAFT photocatalyst from the reticular assembled Zr-porphyrinic metal-organic frameworks (MOFs), along with a biomacromolecule-based chain transfer agent, as efficient bioconjugation tools in water.