T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality.

Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Toxicologic effect and transcriptome analysis for sub-chronic exposure to carbendazim, prochloraz, and their combination on the liver of mice.

Carbendazim (CBZ) and prochloraz (PCZ) are broad-spectrum fungicides used in agricultural peat control. Both fungicides leave large amounts of residues in fruits and are toxic to non-target organisms. However, the combined toxicity of the fungicides to non-target organisms is still unknown. Therefore, we characterized the toxic effects of dietary supplementation with CBZ, PCZ, and their combination for 90 days in 6-week-old male Institute of Cancer Research (ICR) mice. CBZ-H (100 mg/kg day), PCZ-H (10 mg/kg day), and their combination treatments increased the relative liver weights and caused liver injury. The serum total cholesterol (TC), triglyceride (TG), glucose (Glu), pyruvate (PYR), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) levels were reduced, and synergistic toxicity was observed. Hepatic transcriptome revealed that 326 differentially expressed genes (DEGs) of liver were observed in the CBZ treatment group, 149 DEGs in the PCZ treatment group, and 272 DEGs in the combination treatment group. According to KEGG enrichment analysis, the fungicides and their combination affected lipid metabolism, amino acid metabolism, and ferroptosis. In addition, the relative mRNA levels of key genes involved in lipid metabolism were also examined. Compared with individual exposure, combined exposure to CBZ and PCZ caused a more obvious decrease in the expression of some genes related to glycolipid metabolism. Furthermore, the relative mRNA levels of some key genes in the combination treatment group were lower than those in the CBZ and PCZ treated groups. In summary, CBZ, PCZ, and their combination generally caused hepatotoxicity and glycolipid metabolism disorders, which could provide new insights for investigating the combined toxicity of multiple fungicides to animals.

Identifying the active sites in unequal iron-nitrogen single-atom catalysts.

Single-atom catalysts (SACs) have become one of the most attractive frontier research fields in catalysis and energy conversion. However, due to the atomic heterogeneity of SACs and limitations of ensemble-averaged measurements, the essential active sites responsible for governing specific catalytic properties and mechanisms remain largely concealed. In this study, we develop a quantitative method of single-atom catalysis-fluorescence correlation spectroscopy (SAC-FCS), leveraging the atomic structure-dependent catalysis kinetics and single-turnover resolution of single-molecule fluorescence microscopy. This method enables us to investigate the oxidase-like single-molecule catalysis on unidentical iron-nitrogen (Fe-N) coordinated SACs, quantifying the active sites and their kinetic parameters. The findings reveal the significant differences of single sites from the average behaviors and corroborate the oxidase-like catalytic mechanism of the Fe-N active sites. We anticipate that the method will give essential insights into the rational design and application of SACs.

Molecular cloning and functional analysis of Chinese bayberry MrSPL4 that enhances growth and flowering in transgenic tobacco.

Chinese bayberry (Myrica rubra) is an important tree in South China, with its fruit being of nutritional and high economic value. In this study, early ripening (ZJ), medium ripening (BQ) and late ripening (DK) varieties were used as test materials. Young leaves of ZJ, BQ and DK in the floral bud morphological differentiation periods were selected for transcriptome sequencing to excavate earliness related genes. A total of 4,538 differentially expressed genes were detected. Based on clustering analysis and comparisons with genes reportedly related to flowering in Arabidopsis thaliana, 25 homologous genes were identified. Of these, one gene named MrSPL4 was determined, with its expression down-regulated in DK but up-regulated in ZJ and BQ. MrSPL4 contained SBP domain and the target site of miR156, and its total and CDS length were 1,664 bp and 555 bp respectively. The overexpression vector of MrSPL4 (35S::35S::MrSPL4-pCambia2301-KY) was further constructed and successfully transfected into tobacco to obtain MrSPL4-positive plants. Based on the results of qRT-PCR, the relative expression of MrSPL4 was up regulated by 3,862.0-5,938.4 times. Additionally, the height of MrSPL4-positive plants was also significantly higher than that of wild-type (WT), with the bud stage occurring 12 days earlier. Altogether, this study identified an important gene -MrSPL4 in Chinese bayberry, which enhanced growth and flowering, which provided important theoretical basis for early-mature breeding of Chinese bayberry.

Alcohol extracts of Chinese bayberry branch induce S-phase arrest and apoptosis in HepG2 cells.

The alcohol extracts of Chinese bayberry (Myrica rubra) branches (MRBE) are rich in flavonoids which have a variety of medicinal benefits, but their effects on human HepG2 were unknown. In this study, the effects of MRBE on HepG2 cell growth and its potential for inhibiting cancer were explored. The results displayed that MRBE inhibited HepG2 proliferation both by arresting cells in S phase and promoting apoptosis. Quantitative reverse-transcription PCR (qRT-PCR), western blotting, and immunofluorescence showed that MRBE induced S-phase arrest by upregulating p21, which in turn downregulated cyclin and cyclin-dependent kinase messenger RNA (mRNA) and protein. Apoptosis was induced by blocking the expression of BCL-2 and suppression of the Raf/ERK1 signaling pathways. These results indicated that MRBE may have the potential for treatment of human liver cancer, highlighting novel approaches for developing new pharmacological tools for the treatment of this deadly type cancer. Meanwhile, it provides a new direction for the medicinal added values of Chinese bayberry, which helped to broaden the diversified development of its industry chain.

Effects of Enhanced Resistance and Transcriptome Analysis of Twig Blight Disease by Exogenous Brassinolide in Myrica rubra.

Twig blight disease is the primary disease that affects the production of Myrica rubra in China. It was reported that exogenous brassinolide (BL) can improve disease resistance in plants. Here, we examined the effects of exogenous BL on disease resistance, chlorophyll contents, antioxidant enzyme activity, ROS accumulation, and key gene expression of M. rubra to analyze the mechanism of BR-induced resistance of twig blight disease in M. rubra. The results demonstrated that 2.0 mg·L-1 of BL could significantly lessen the severity of twig blight disease in M. rubra. Exogenous BL increased the contents of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll. Moreover, exogenous BL also significantly enhanced the activity of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and decreased malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation in leaves, such as H2O2 and O2·-. Additionally, exogenous BL dramatically up-regulated the expression of pathogenesis-related (PR) genes such as MrPR1, MrPR2, and MrPR10, as well as important genes such as MrBAK1, MrBRI1, and MrBZR1 involved in brassinosteroid (BR) signaling pathway. The transcriptome analysis revealed that a total of 730 common differentially expressed genes (DEGs) under BL treatment were found, and these DEGs were primarily enriched in four Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on these findings, nine important candidate genes related to the resistance of twig blight disease under BL treatment were further identified. In this study, we elucidated the effects of exogenous BL on enhancing the resistance of M. rubra to twig blight disease and preliminary analyzed the potential mechanism of resistance induction, which will provide a crucial foundation for the management and prevention of twig blight disease in M. rubra.

Kinetically restrained oxygen reduction to hydrogen peroxide with nearly 100% selectivity.

Hydrogen peroxide has been synthesized mainly through the electrocatalytic and photocatalytic oxygen reduction reaction in recent years. Herein, we synthesize a single-atom rhodium catalyst (Rh1/NC) to mimic the properties of flavoenzymes for the synthesis of hydrogen peroxide under mild conditions. Rh1/NC dehydrogenates various substrates and catalyzes the reduction of oxygen to hydrogen peroxide. The maximum hydrogen peroxide production rate is 0.48 mol gcatalyst-1 h-1 in the phosphorous acid aerobic oxidation reaction. We find that the selectivity of oxygen reduction to hydrogen peroxide can reach 100%. This is because a single catalytic site of Rh1/NC can only catalyze the removal of two electrons per substrate molecule; thus, the subsequent oxygen can only obtain two electrons to reduce to hydrogen peroxide through the typical two-electron pathway. Similarly, due to the restriction of substrate dehydrogenation, the hydrogen peroxide selectivity in commercial Pt/C-catalyzed enzymatic reactions can be found to reach 75%, which is 30 times higher than that in electrocatalytic oxygen reduction reactions.

Identifying Luminol Electrochemiluminescence at the Cathode via Single-Atom Catalysts Tuned Oxygen Reduction Reaction.

Luminol-based electrochemiluminescence (ECL) can be readily excited by various reactive oxygen species (ROS) electrogenerated with an oxygen reduction reaction (ORR). However, the multiple active intermediates involved in the ORR catalyzed with complex nanomaterials lead to recognizing the role of ROS still elusive. Moreover, suffering from the absence of the direct electrochemical oxidation of luminol at the cathode and poor transformation efficiency of O2 to ROS, the weak cathodic ECL emission of luminol is often neglected. Herein, owing to the tunable coordination environment and structure-dependent catalytic feature, single-atom catalysts (SACs) are employed to uncover the relationship between the intrinsic ORR activity and ECL behavior. Interestingly, the traditionally negligible cathodic ECL of luminol is first boosted (ca. 70-fold) owing to the combination of electrochemical ORR catalyzed via SACs and chemical oxidation of luminol. The boosted cathodic ECL emission exhibits electron-transfer pathway-dependent response by adjusting the surrounding environment of the center metal atoms in a controlled way to selectively produce different active intermediates. This work bridges the relationship between ORR performance and ECL behavior, which will guide the development of an amplified sensing platform through rational tailoring of the ORR activity of SACs and potential-resolved ECL assays based on the high-efficiency cathodic ECL reported.

Bubble-templated synthesis of nanocatalyst Co/C as NADH oxidase mimic.

Designing highly active nanozymes for various enzymatic reactions remains a challenge in practical applications and fundamental research. In this work, by studying the catalytic functions of natural NADH oxidase (NOX), we devised and synthesized a porous carbon-supported cobalt catalyst (Co/C) to mimic NOX. The Co/C can catalyze dehydrogenation of NADH and transfers electrons to O2 to produce H2O2. Density functional theory calculations reveal that the Co/C can catalyze O2 reduction to H2O2 or H2O considerably. The Co/C can also mediate electron transfer from NADH to heme protein cytochrome c, thereby exhibiting cytochrome c reductase-like activity. The Co/C nanoparticles can deplete NADH in cancer cells, induce increase of the reactive oxygen species, lead to impairment of oxidative phosphorylation and decrease in mitochondrial membrane potential, and cause ATP production to be damaged. This 'domino effect' facilitates the cell to approach apoptosis.

An overview of the nutritional value, health properties, and future challenges of Chinese bayberry.

Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.

Physics of biomolecular recognition and conformational dynamics.

Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.

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Twig blight is a serious disease of bayberry, which limits bayberry production. In order to prevent and manage the disease, we used high-throughput sequencing technology to analyze bacterial and fungal community richness and diversity in various organs of the tree, bulk and rhizosphere soil of healthy and diseased bayberry. The results showed significant differences in richness and diversity of bacteria and fungi in bulk soil, rhizosphere soil, roots, trunks, barks, and leaves between twig blight diseased trees and healthy trees. In bulk soil, the richness and diversity of bacteria significantly decreased, while that of fungi significantly increased. In barks of diseased trees, the richness and diversity of bacteria significantly increased, and those of fungi significantly decreased. The relative abundance of dominant bacteria and fungi in various organs, bulk soil, and root surface soil changed significantly at phylum, class, and genus levels in the diseased trees. The relative abundance of Pseudomonas sp. on the trunks, roots, and root surface soils of diseased trees significantly decreased, and Fusarium sp. of the diseased root surface and bulk soils also significantly decreased, while the relative abundance of Penicillium sp. on the diseased root surface and bulk soils significantly increased. Pestalotiopsis sp., from the same genus as the twig blight pathogen, was less abundant in the roots but more abundant in the leaves, trunks, barks as well as root surface soils and bulk soils of the diseased bayberry trees than those of the health trees. The relative abundance of Pestalotiopsis sp. was positively correlated with those of most of the fungi. Our results might provide useful theoretical basis for the development of ecological improvement and healthy-tree cultivation technology, and biological control of bayberry twig blight disease.

The Damage Caused by Decline Disease in Bayberry Plants through Changes in Soil Properties, Rhizosphere Microbial Community Structure and Metabolites.

Decline disease causes serious damage and rapid death in bayberry, an important fruit tree in south China, but the cause of this disease remains unclear. The aim of this study was to investigate soil quality, microbial community structure and metabolites of rhizosphere soil samples from healthy and diseased trees. The results revealed a significant difference between healthy and diseased bayberry in soil properties, microbial community structure and metabolites. Indeed, the decline disease caused a 78.24% and 78.98% increase in Rhizomicrobium and Cladophialophora, but a 28.60%, 57.18%, 38.84% and 68.25% reduction in Acidothermus, Mortierella, Trichoderma and Geminibasidium, respectively, compared with healthy trees, based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of bacterial and fungal communities included pH, organic matter, magnesium, available phosphorus, nitrogen and calcium, which exhibited a greater influence in bacterial communities than in fungal communities. In addition, there was a high correlation between the changes in microbial community structure and secondary metabolites. Indeed, GC-MS metabolomics analysis showed that the healthy and diseased samples differed over six metabolic pathways, including thiamine metabolism, phenylalanine-tyrosine-tryptophan biosynthesis, valine-leucine-isoleucine biosynthesis, phenylalanine metabolism, fatty acid biosynthesis and fatty acid metabolism, where the diseased samples showed a 234.67% and 1007.80% increase in palatinitol and cytidine, respectively, and a 17.37-8.74% reduction in the other 40 metabolites compared to the healthy samples. Overall, these results revealed significant changes caused by decline disease in the chemical properties, microbiota and secondary metabolites of the rhizosphere soils, which provide new insights for understanding the cause of this bayberry disease.

The bayberry database: a multiomic database for Myrica rubra, an important fruit tree with medicinal value.

BACKGROUND: Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important fruit tree in China, and has high medicinal value. At present, the genome, transcriptome and germplasm resources of bayberry have been reported. In order to make more convenient use of these data, the Bayberry Database was established. RESULTS: The Bayberry Database is a comprehensive and intuitive data platform for examining the diverse annotated genome and germplasm resources of this species. This database contains nine central functional domains to interact with multiomic data: home, genome, germplasm, markers, tools, map, expression, reference, and contact. All domains provide pathways to a variety of data types composed of a reference genome sequence, transcriptomic data, gene patterns, phenotypic data, fruit images of Myrica rubra varieties, gSSR data, gene maps with annotation and evolutionary analyses. The tools module includes BLAST search, keyword search, sequence fetch and enrichment analysis functions. CONCLUSIONS: The web address of the database is as follows http://www.bayberrybase.cn/ . The Myrica rubra database is an intelligent, interactive, and user-friendly system that enables researchers, breeders and horticultural personnel to browse, search and retrieve relevant and useful information and thus facilitate genomic research and breeding efforts concerning Myrica rubra. This database will be of great help to bayberry research and breeding in the future.

Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry (Myrica rubra).

Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.

Interfacial Electron Engineering of Palladium and Molybdenum Carbide for Highly Efficient Oxygen Reduction.

Interfacial electron engineering between noble metal and transition metal carbide is identified as a powerful strategy to improve the intrinsic activity of electrocatalytic oxygen reduction reaction (ORR). However, this short-range effect and the huge structural differences make it a significant challenge to obtain the desired electrocatalyst with atomically thin noble metal layers. Here, we demonstrated the combinatorial strategies to fabricate the heterostructure electrocatalyst of Mo2C-coupled Pd atomic layers (AL-Pd/Mo2C) by precise control of metal-organic framework confinement and covalent interaction. Both atomic characterizations and density functional theory calculations uncovered that the strong electron effect imposed on Pd atomic layers has intensively regulated the electronic structures and d-band center and then optimized the reaction kinetics. Remarkably, AL-Pd/Mo2C showed the highest ORR electrochemical activity and stability, which delivered a mass activity of 2.055 A mgPd-1 at 0.9 V, which is 22.1, 36.1, and 80.3 times higher than Pt/C, Pd/C, and Pd nanoparticles, respectively. The present work has developed a novel approach for atomically noble metal catalysts and provides new insights into interfacial electron regulation.

Discovery of Small Molecule NSC290956 as a Therapeutic Agent for KRas Mutant Non-Small-Cell Lung Cancer.

HRas-GTP has a transient intermediate state with a "non-signaling open conformation" in GTP hydrolysis and nucleotide exchange. Due to the same hydrolysis process and the structural homology, it can be speculated that the active KRas adopts the same characteristics with the "open conformation." This implies that agents locking this "open conformation" may theoretically block KRas-dependent signaling. Applying our specificity-affinity drug screening approach, NSC290956 was chosen by high affinity and specificity interaction with the "open conformation" structure HRasG60A-GppNp. In mutant KRas-driven non-small-cell lung cancer (NSCLC) model system, NSC290956 effectively suppresses the KRas-GTP state and gives pharmacological KRas inhibition with concomitant blockages of both the MAPK-ERK and AKT-mTOR pathways. The dual inhibitory effects lead to the metabolic phenotype switching from glycolysis to mitochondrial metabolism, which promotes the cancer cell death. In the xenograft model, NSC290956 significantly reduces H358 tumor growth in nude mice by mechanisms similar to those observed in the cells. Our work indicates that NSC290956 can be a promising agent for the mutant KRas-driven NSCLC therapy.

Link prediction in recommender systems with confidence measures.

The link prediction aims at predicting missing or future links in networks, which provides theoretical significance and extensive applications in the related field. However, the degree of confidence in the prediction results has not been fully discussed in related works. In this article, we propose a similarity confidence coefficient and a confidence measure for link prediction. The former is used to balance the reliability of similarity calculation results, which might be untrustworthy due to the information asymmetry in the calculation, and also makes it easier to achieve the optimal accuracy with a smaller number of neighbors. The latter is used to quantify our confidence in the prediction results of each prediction. The experimental results based on the Movie-Lens data set show that prediction accuracy is improved when the similarity between the nodes is corrected by the similarity confidence coefficient. Second, the experiments also confirm that the confidence degree of the link prediction results can be measured quantitatively. Our research indicates that the confidence level on each prediction is determined by the amount of data used in the corresponding calculation, which can be measured quantitatively.

Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry.

BACKGROUND: Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. Elucidating the genetic basis of the biosynthesis of active antioxidant compounds in bayberry is fundamental for genetic improvement of bayberry and industrial applications of the fruit's antioxidant components. Here, we report the genome sequence of a multiple disease-resistant bayberry variety, 'Zaojia', in China, and the transcriptome dynamics in the course of fruit development. RESULTS: A 289.92 Mb draft genome was assembled, and 26,325 protein-encoding genes were predicted. Most of the M. rubra genes in the antioxidant signaling pathways had multiple copies, likely originating from tandem duplication events. Further, many of the genes found here present structural variations or amino acid changes in the conserved functional residues across species. The expression levels of antioxidant genes were generally higher in the early stages of fruit development, and were correlated with the higher levels of total flavonoids and antioxidant capacity, in comparison with the mature fruit stages. Based on both gene expression and biochemical analyses, five genes, namely, caffeoyl-CoA O-methyltransferase, anthocyanidin 3-O-glucosyltransferase, (+)-neomenthol dehydrogenase, gibberellin 2-oxidase, and squalene monooxygenase, were suggested to regulate the flavonoid, anthocyanin, monoterpenoid, diterpenoid, and sesquiterpenoid/triterpenoid levels, respectively, during fruit development. CONCLUSIONS: This study describes both the complete genome and transcriptome of M. rubra. The results provide an important basis for future research on the genetic improvement of M. rubra and contribute to the understanding of its genetic evolution. The genome sequences corresponding to representative antioxidant signaling pathways can help revealing useful traits and functional genes.

Synthesis of adenosine analogues with indole moiety as human adenosine A3 receptor ligands.

Adenosine is an endogenous modulator exerting its functions through the activation of four adenosine receptor (AR) subtypes, termed A1, A2A, A2B and A3, which belong to the G-protein-coupled receptor superfamily. The human A3AR (hA3AR) subtype is implicated in several cytoprotective functions. Therefore, hA3AR modulators, and in particular agonists, are sought for their potential application as anti-inflammatory, anti-cancer and cardioprotective agents. Here, we prepared novel adenosine derivatives with indole moiety as hA3AR ligands. According to the biological assay, we found that 2-substituents 11 were critical structural determinants for A3AR ligands (Ki = 111 nM). The observed structure-affinity relationships of this class of ligands were also exhaustively rationalized using the molecular modelling approach. This allows the investigation on the binding mode of the potential compound in the ligand-binding pocket of the human A3 receptor. The results demonstrated that 11 can interact with the ASN250, GLN167, PHE168 and VAL178 through hydrogen bonding, which are shown to be important for ligand-receptor interaction.