In Situ Encapsulation of Cytochrome c within Covalent Organic Frames Using Deep Eutectic Solvents under Ambient Conditions.

In situ integration of enzymes with covalent organic frameworks (COFs) to form hybrid biocatalysts is both significant and challenging. In this study, we present an innovative strategy employing deep eutectic solvents (DESs) to synergistically synthesize COFs and shield cytochrome c (Cyt c). By utilizing DESs as reaction solvents in combination with water, we successfully achieved rapid and in situ encapsulation of Cyt c within COFs (specifically COF-TAPT-TFB) under ambient conditions. The resulting Cyt c@COF-TAPT-TFB composite demonstrates a remarkable preservation of enzymatic activity. This encapsulation strategy also imparts exceptional resistance to organic solvents and exhibits impressive recycling stability. Additionally, the enhanced catalytic efficiency of Cyt c@COF-TAPT-TFB in a photoenzymatic cascade reaction is also showcased.

High-efficiency plasmonic vortex generation with near-infrared bifunctional metasurfaces.

Plasmonic vortices have shown a wide range of applications in on-chip photonics due to their fascinating properties of the orbital angular momenta (OAM) and phase singularity. However, conventional devices to generate them suffer from issues of low efficiencies and limited functionalities. Here, we establish a systematic scheme to construct high-efficiency bifunctional metasurfaces that can generate two plasmonic vortices exhibiting distinct topological charges, based on a series of reflective meta-atoms exhibiting tailored reflection-phases dictated by both resonant and geometric origins. As a benchmark test, we first construct a meta-coupler with meta-atoms exhibiting geometric phases only, and experimentally demonstrate that it can generate a pre-designed plasmonic vortex at the wavelength of 1064 nm with an efficiency of 27% (56% in simulation). Next, we design/fabricate two bifunctional metasurfaces with meta-atoms integrated with both resonant and geometric phases, and experimentally demonstrate that they can generate divergent (or focused) or convergent (or defocused) plasmonic vortices with district OAM as shined by circularly polarized light with opposite helicity at 1064 nm wavelength. Our work provides an efficient platform to generate plasmonic vortices as desired, which can find many applications in on-chip photonics.

Building ecological civilization: the importance of promoting green investments by Chinese companies.

The study investigated "Building Ecological Civilization: the Importance of Promoting Green Investments by Chinese Companies" to examine the complex connections between the factors affecting Chinese businesses' ecological performance (EP). An autoregressive distributed lag (ARDL) model is used in the study to analyze the impact of green investments (GI), the policy environment (PE), government support (GS), public awareness and perception (PAP), and technological capability (TC) on companies' earnings per share (EPS). The results show a strong correlation between GI and EP, indicating that businesses' growing use of green initiatives is essential for raising environmental sustainability. The study also shows that PE, TC, and EP have an inverse relationship, indicating the need for more supportive governmental policies and regulations and the effective adoption and implementation of green technologies. The interaction of GS and PAP significantly reduces the ecological impact of green investments, highlighting the significance of citizen involvement and the role of government in advancing ecological civilization. The findings also demonstrated that green investments, policy environments, public perception, and technology influence the ecological performance of businesses. They also demonstrate statistical robustness with low p-values. This information is essential for developing policies that support an ecological civilization, which is necessary for China and globally in light of the current climate crisis.

Evolution Characteristics of the Microstructure with Different Fracturing Fluids: An Experimental Study of Guizhou Bituminous Coal.

Fracturing fluid is a key factor affecting the hydraulic fracture morphology and coal microstructure, which plays a key role in the hydraulic fracturing effect. To compare the effect of clean water, clean fracturing fluid, and acid fracturing fluid on the pore structure of coal, this paper used high-pressure mercury injection (MIP), low-temperature N2 adsorption (LT-N2A), and scanning electron microscopy (SEM) to determine the pore structure of Guizhou bituminous coal before and after the action of fracturing fluid. The results show that clean water can cause mineral expansion and reduce pore volume by about 6% and clean fracturing fluid and acid fracturing fluid can increase pore volume by 3 and 12%, respectively, due to different degrees of acidity. The MIP data show that the pore structure of coal samples is more complex after the action of different fracturing fluids, and acidic fracturing fluids can increase the fractal dimension of the pore by about 7%. The LT-N2A data showed that the fractal dimension of micropores and transition pores decreased after the action of different fracturing fluids. In general, acid fracturing fluid has the best effect on the coal microstructure, followed by clean fracturing fluid, and the least effect on clean water.

CGUN-2A: Deep Graph Convolutional Network via Contrastive Learning for Large-Scale Zero-Shot Image Classification.

Taxonomy illustrates that natural creatures can be classified with a hierarchy. The connections between species are explicit and objective and can be organized into a knowledge graph (KG). It is a challenging task to mine features of known categories from KG and to reason on unknown categories. Graph Convolutional Network (GCN) has recently been viewed as a potential approach to zero-shot learning. GCN enables knowledge transfer by sharing the statistical strength of nodes in the graph. More layers of graph convolution are stacked in order to aggregate the hierarchical information in the KG. However, the Laplacian over-smoothing problem will be severe as the number of GCN layers deepens, which leads the features between nodes toward a tendency to be similar and degrade the performance of zero-shot image classification tasks. We consider two parts to mitigate the Laplacian over-smoothing problem, namely reducing the invalid node aggregation and improving the discriminability among nodes in the deep graph network. We propose a top-k graph pooling method based on the self-attention mechanism to control specific node aggregation, and we introduce a dual structural symmetric knowledge graph additionally to enhance the representation of nodes in the latent space. Finally, we apply these new concepts to the recently widely used contrastive learning framework and propose a novel Contrastive Graph U-Net with two Attention-based graph pooling (Att-gPool) layers, CGUN-2A, which explicitly alleviates the Laplacian over-smoothing problem. To evaluate the performance of the method on complex real-world scenes, we test it on the large-scale zero-shot image classification dataset. Extensive experiments show the positive effect of allowing nodes to perform specific aggregation, as well as homogeneous graph comparison, in our deep graph network. We show how it significantly boosts zero-shot image classification performance. The Hit@1 accuracy is 17.5% relatively higher than the baseline model on the ImageNet21K dataset.

Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development.

Mucuna pruriens, commonly called velvet bean, is the main natural source of levodopa (L-DOPA), which has been marketed as a psychoactive drug for the clinical management of Parkinson's disease and dopamine-responsive dystonia. Although velvet bean is a very important plant species for food and pharmaceutical manufacturing, the lack of genetic and genomic information about this species severely hinders further molecular research thereon and biotechnological development. Here, we reported the first velvet bean genome, with a size of 500.49 Mb and 11 chromosomes encoding 28,010 proteins. Genomic comparison among legume species indicated that velvet bean speciated ∼29 Ma from soybean clade, without specific genome duplication. Importantly, we identified 21 polyphenol oxidase coding genes that catalyse l-tyrosine to L-DOPA in velvet bean, and two subfamilies showing tandem expansion on Chr3 and Chr7 after speciation. Interestingly, disease-resistant and anti-pathogen gene families were found contracted in velvet bean, which might be related to the expansion of polyphenol oxidase. Our study generated a high-quality genomic reference for velvet bean, an economically important agricultural and medicinal plant, and the newly reported L-DOPA biosynthetic genes could provide indispensable information for the biotechnological and sustainable development of an environment-friendly L-DOPA biosynthesis processing method.

Evolution of coastal forests based on a full set of mangrove genomes.

Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences of 30 additional species, comprising almost all mangroves globally. These community-wide genomic data will be valuable for ecology, evolution and biodiversity research. While the data revealed 27 independent origins of mangroves, the total phylogeny shows only modest increases in species number, even in coastal areas of active speciation, suggesting that mangrove extinction is common. A possible explanation for common extinction is the frequent sea-level rises and falls (SLRs and SLFs) documented in the geological record. Indeed, near-extinctions of species with extremely small population size (N) often happened during periods of rapid SLR, as revealed by the genome-wide heterozygosity of almost all mangroves. Reduction in N has possibly been further compounded by population fragmentation and the subsequent accumulation of deleterious mutations, thus pushing mangroves even closer to extinction. Crucially, the impact of the next SLR will be exacerbated by human encroachment into these mangrove habitats, potentially altering the ecosystems of tropical coasts irreversibly.

Understanding Pixel-Level 2D Image Semantics With 3D Keypoint Knowledge Engine.

Pixel-level 2D object semantic understanding is an important topic in computer vision and could help machine deeply understand objects (e.g., functionality and affordance) in our daily life. However, most previous methods directly train on correspondences in 2D images, which is end-to-end but loses plenty of information in 3D spaces. In this paper, we propose a new method on predicting image corresponding semantics in 3D domain and then projecting them back onto 2D images to achieve pixel-level understanding. In order to obtain reliable 3D semantic labels that are absent in current image datasets, we build a large scale keypoint knowledge engine called KeypointNet, which contains 103,450 keypoints and 8,234 3D models from 16 object categories. Our method leverages the advantages in 3D vision and can explicitly reason about objects self-occlusion and visibility. We show that our method gives comparative and even superior results on standard semantic benchmarks.

Extracellular PKM2 facilitates organ-tissue fibrosis progression.

Persistent activation of fibroblasts and resistance of myofibroblasts to turnover play important roles in organ-tissue fibrosis development and progression. The mechanism that mediates apoptosis resistance of myofibroblasts is not understood. Here, we report that myofibroblasts express and secrete PKM2. Extracellular PKM2 (EcPKM2) facilitates progression of fibrosis by protecting myofibroblasts from apoptosis. EcPKM2 upregulates arginase-1 expression in myofibroblasts and therefore facilitates proline biosynthesis and subsequent collagen production. EcPKM2 interacts with integrin αvß3 on myofibroblasts to activate FAK-PI3K signaling axis. Activation of FAK-PI3K by EcPKM2 activates downstream NF-κB survival pathway to prevent myofibroblasts from apoptosis. On the other hand, activation of FAK- PI3K by EcPKM2 suppresses PTEN to subsequently upregulate arginase-1 in myofibroblasts. Our studies uncover an important mechanism for organ fibrosis progression. More importantly, an antibody disrupting the interaction between PKM2 and integrin αvß3 is effective in reversing fibrosis, suggesting a possible therapeutic strategy and target for treatment of organ fibrosis.

Study of quickly separating water from tunneling slurry waste by combining vacuum with electro-osmosis.

Tunneling slurry waste causes multiple problems, including environmental pollution, and requires transportation and a large landfill space, and therefore, it is important to find a method that can quickly separate water from tunneling slurry waste for metro construction. This paper proposes a practical method to improve the effect of slurry waste separation by implementing five laboratory tests. The results of these tests reflect that vacuum combined electro-osmosis is a suitable and practical method for treating tunneling slurry waste. The water content after treatment by vacuum combined horizontal electric field electro-osmosis method is not only lower than that after other methods but also close to the liquid limit, which fully meets the requirements of engineering transportation. However, vacuum and filter press dewatering cannot give full play to the drainage effect when the slurry permeability coefficient is too low. This combined technique can improve water separation from the slurry and works well in engineering applications.

Pyruvate Kinase M2 Coordinates Metabolism Switch between Glycolysis and Glutaminolysis in Cancer Cells.

Cancer cells alter their nutrition metabolism to cope the stressful environment. One important metabolism adjustment is that cancer cells activate glutaminolysis in response to the reduced carbon from glucose entering into the TCA cycle due to inactivation of several enzymes in glycolysis. An important question is how the cancer cells coordinate the changes of glycolysis and glutaminolysis. In this report, we demonstrate that the pyruvate kinase inactive dimer PKM2 facilitates activation of glutaminolysis. Our experiments show that growth stimulations promote PKM2 dimer. The dimer PKM2 plays a role in regulation of glutaminolysis by upregulation of mitochondrial glutaminase I (GLS-1). PKM2 dimer regulates the GLS-1 expression by controlling internal ribosome entry site (IRES)-dependent c-myc translation. Growth stimulations promote PKM2 interacting with c-myc IRES-RNA, thus facilitating c-myc IRES-dependent translation. Our study reveals an important linker that coordinates the metabolism adjustment in cancer cells.

Lineage-specific evolution of mangrove plastid genomes.

Mangroves is an umbrella term for plants located across the tropics and sub-tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage-specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic clades. We demonstrate that chloroplast gene order, content, and genome size is largely conserved in mangroves. The exceptions are loss of the photosystem I gene psaZ in Acanthus ilicifolius and inversion of the ribosomal protein gene rpl23 in Avicennia germinans. The repeat content of mangrove chloroplast varied between species, but was conserved within species of the same order. Sequence diversity analysis revealed that the IR (invert repeat) region was highly conserved compared to the SC (single-copy) region in most phylogenetic clades, except clade core leptosporangiates (ferns). The ribosomal protein gene rps7 was under positive selection in Kandelia obovato, Rhizophora stylosa, Bruguiera sexangular and Rhizophora mangle, a monophyletic branch of clade fabids, while no evidence of positive selection was found in other mangrove lineages. Taken together, our data suggests that convergent evolutionary dynamics leaves no significant signal on the plastid genome of mangroves. The complete chloroplast genomes provided in this study shed light on the evolution of these important plastids and provides a valuable resource for further research efforts.

Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses.

Mangroves are a group of plant species that occupy the coastal intertidal zone and are major components of this ecologically important ecosystem. Mangroves belong to about twenty diverse families. Here, we sequenced and assembled chloroplast genomes of 14 mangrove species from eight families spanning five rosid orders and one asterid order: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, and Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, and Thespesia populnea), Myrtales (Laguncularia racemosa, Sonneratia ovata, and Pemphis acidula), and Sapindales (Xylocarpus moluccensis). These chloroplast genomes range from 149 kb to 168 kb in length. A conserved structure of two inverted repeats (IRa and IRb, ~25.8 kb), one large single-copy region (LSC, ~89.0 kb), and one short single-copy region (SSC, ~18.9 kb) as well as ~130 genes (85 protein-coding, 37 tRNAs, and 8 rRNAs) was observed. We found the lowest divergence in the IR regions among the four regions. We also identified simple sequence repeats (SSRs), which were found to be variable in numbers. Most chloroplast genes are highly conserved, with only four genes under positive selection or relaxed pressure. Combined with publicly available chloroplast genomes, we carried out phylogenetic analysis and confirmed the previously reported phylogeny within rosids, including the positioning of obscure families in Malpighiales. Our study reports 14 mangrove chloroplast genomes and illustrates their genome features and evolution.

Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1.

Penicillium is an ascomycetous genus widely distributed in the natural environment and is one of the dominant fungi involved in the decomposition of mangroves, which can produce a variety of antitumor compounds and bioactive substances. However, in mangrove ecosystems there is no complete genome in this genus. In this study, we isolated a fungus strain named Penicillium variabile HXQ-H-1 from coast mangrove (Fujian Province, China). We generated a chromosome-level genome with total size of 33.32 Mb, scaffold N50 of 5.23 Mb and contig N50 of 96.74 kb. Additionally, we anchored about 95.91% assembly sequences into the longest seven scaffolds, and predicted 10,622 protein-coding genes, in which 99.66% could be annotated by eight protein databases. The secondary metabolites analysis reveals the strain has various gene clusters involving polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and terpene synthase that may have a largely capacity of biotechnological potential. Comparison genome analysis between Penicillium variabile and Talaromyces islandicus reveals a small difference in the total number of genes, whereas HXQ-H-1 has a higher gene number with COG functional annotation. Evolutionary relationship of Penicillum based on genome-wide data was carried out for the first time, showing the strain HXQ-H-1 is closely related to Talaromyces islandicus. This genomic resource may provide a new resource for development of novel bioactive antibiotics, drug candidates and precursors in Penicillium variabile.

The genetic architecture of floral traits in the woody plant Prunus mume.

Mei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Here, we investigate the genetic architecture of floral traits in mei and its domestication history by sampling and resequencing a total of 351 samples including 348 mei accessions and three other Prunus species at an average sequencing depth of 19.3×. Highly-admixed population structure and introgression from Prunus species are identified in mei accessions. Through a genome-wide association study (GWAS), we identify significant quantitative traits locus (QTLs) and genomic regions where several genes, such as MYB108, are positively associated with petal color, stigma color, calyx color, and bud color. Results from this study shed light on the genetic basis of domestication in flowering plants, particularly woody plants.

Natural Product Micheliolide (MCL) Irreversibly Activates Pyruvate Kinase M2 and Suppresses Leukemia.

Metabolic reprogramming of cancer cells is essential for tumorigenesis in which pyruvate kinase M2 (PKM2), the low activity isoform of pyruvate kinase, plays a critical role. Herein, we describe the identification of a nature-product-derived micheliolide (MCL) that selectively activates PKM2 through the covalent binding at residue cysteine424 (C424), which is not contained in PKM1. This interaction promotes more tetramer formation, inhibits the lysine433 (K433) acetylation, and influences the translocation of PKM2 into the nucleus. In addition, the pro-drug dimethylaminomicheliolide (DMAMCL) with similar properties as MCL significantly suppresses the growth of leukemia cells and tumorigenesis in a zebrafish xenograft model. Cell-based assay with knock down PKM2 expression verifies that the effects of MCL are dependent on PKM2 expression. DMAMCL is currently in clinical trials in Australia. Our discovery may provide a valuable pharmacological mechanism for clinical treatment and benefit the development of new anticancer agents.

The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.

Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata.

Rhodiola crenulata, a well-known medicinal Tibetan herb, is mainly grown in high-altitude regions of the Tibet, Yunnan, and Sichuan provinces in China. In the past few years, increasing numbers of studies have been published on the potential pharmacological activities of R. crenulata, strengthening our understanding into its putitive active ingredient composition, pharmacological activity, and mechanism of action. These findings also provide strong evidence supporting the important medicinal and economical value of R. crenulata. Consequently, some Rhodiola species are becoming endangered because of overexploitation and environmental destruction. However, little is known about the genetic and genomic information of any Rhodiola species. Here we report the first draft assembly ofthe R. crenulata genome, which was 344.5 Mb (25.7 Mb Ns), accounting for 82% of the estimated genome size, with a scaffold N50 length of 144.7 kb and a contig N50 length of 25.4 kb. The R. crenulata genome is not only highly heterozygous but also highly repetitive, with ratios of 1.12% and 66.15%, respectively, based on the k-mer analysis. Furthermore, 226.6 Mb of transposable elements were detected, of which 77.03% were long terminal repeats. In total, 31 517 protein-coding genes were identified, capturing 86.72% of expected plant genes in BUSCO. Additionally, 79.73% of protein-coding genes were functionally annotated. R. crenulata is an important medicinal plant and also a potentially interesting model species for studying the adaptability of Rhodiola species to extreme environments. The genomic sequences of R. crenulata will be useful for understanding the evolutionary mechanism of the stress resistance gene and the biosynthesis pathways of the different medicinal ingredients, for example, salidroside in R. crenulata.

PKM2 released by neutrophils at wound site facilitates early wound healing by promoting angiogenesis.

Neutrophils infiltration/activation following wound induction marks the early inflammatory response in wound repair. However, the role of the infiltrated/activated neutrophils in tissue regeneration/proliferation during wound repair is not well understood. Here, we report that infiltrated/activated neutrophils at wound site release pyruvate kinase M2 (PKM2) by its secretive mechanisms during early stages of wound repair. The released extracellular PKM2 facilitates early wound healing by promoting angiogenesis at wound site. Our studies reveal a new and important molecular linker between the early inflammatory response and proliferation phase in tissue repair process.

Loss of Cell Surface CD47 Clustering Formation and Binding Avidity to SIRPα Facilitate Apoptotic Cell Clearance by Macrophages.

CD47, a self recognition marker expressed on tissue cells, interacts with immunoreceptor SIRPα expressed on the surface of macrophages to initiate inhibitory signaling that prevents macrophage phagocytosis of healthy host cells. Previous studies suggested that cells may lose surface CD47 during aging or apoptosis to enable phagocytic clearance. In the current study, we demonstrate that the level of cell surface CD47 is not decreased, but the distribution pattern of CD47 is altered, during apoptosis. On nonapoptotic cells, CD47 molecules are clustered in lipid rafts forming punctates on the surface, whereas on apoptotic cells, CD47 molecules are diffused on the cell surface following the disassembly of lipid rafts. We show that clustering of CD47 in lipid rafts provides a high binding avidity for cell surface CD47 to ligate macrophage SIRPα, which also presents as clusters, and elicits SIRPα-mediated inhibitory signaling that prevents phagocytosis. In contrast, dispersed CD47 on the apoptotic cell surface is associated with a significant reduction in the binding avidity to SIRPα and a failure to trigger SIRPα signal transduction. Disruption of plasma membrane lipid rafts with methyl-ß-cyclodextrin diffuses CD47 clusters, leading to a decrease in the cell binding avidity to SIRPα and a concomitant increase in cells being engulfed by macrophages. Taken together, our study reveals that CD47 normally is clustered in lipid rafts on nonapoptotic cells but is diffused in the plasma membrane when apoptosis occurs; this transformation of CD47 greatly reduces the strength of CD47-SIRPα engagement, resulting in the phagocytosis of apoptotic cells.