In this study, Rh(III)‐catalyzed C−H bifunctionalization and direct vinylene annulation of sulfoxonium ylides and N‐carbamoylindoles with vinylene carbonate was accomplished, which afforded a series ...of naphthalenones containing a β‐ketosulfoxonium ylide moiety, isocoumarins, and pyrimidones. This protocol featured mild conditions, broad substrate scope, and functional‐groups compatibility. In addition, related applications and preliminary mechanistic exploratory were also investigated
Herein, Rh(III)‐catalyzed C4‐selective C−H allylation and prenylation of indoles by using a weak carbonyl coordination directing group have been reported. By employing 5‐methylene‐1,3‐dioxan‐2‐ones, ...4‐vinyl‐1,3‐dioxolan‐2‐ones and 2‐methyl‐2,3‐butadiene as scalable cross‐coupling partners, these divergent synthesis protocols proceed smoothly under redox‐neutral reaction conditions, delivering various allylated and prenylated indoles in moderate to satisfied yields. This transformation exhibits high functional‐groups compatibility and broad substrate scope. Scale‐up experiment and mechanistic studies were also accomplished.
Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for ...all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
This study reports two gap-free reference genomes for Oryza sativa xian/indica varieties ZS97 and MH63, which are used as a model system for studying rice heterosis and yield. Further genomic analyses show that the architectures of functional centromeres are extensively variable at the sequence level. These two gap-free rice genomes provide a new standard for assembling reference genomes of other plant species.
Antituberculosis drug‐induced liver injury (ATDILI) has received increasing attention globally, which may limit the effectiveness of antituberculosis (anti‐TB) treatment. Many host genetic ...determinants of ATDILI have been identified recently. As little knowledge is currently available about the association between aldehyde dehydrogenase 1 family member A1 (ALDH1A1) polymorphisms and ATDILI, the association between their variants and the susceptibility to ATDILI was investigated. A total of 747 patients with TB treated by first‐line anti‐TB drugs were prospectively enrolled at West China Hospital. Genomic DNA was extracted from the peripheral blood sample of each patient and seven single‐nucleotide polymorphisms (SNPs) of ALDH1A1 gene were screened and genotyped with a custom‐designed 2×48‐plex SNP Scan TM kit. The patients were followed up monthly to monitor the development of ATDILI. The C allele and the CA genotype of rs7852860 were significantly associated with an elevated risk for ATDILI (p = .006 and 0.005, respectively), which was consistent with the results in the dominant and additive models. No allele, genotype, or genetic model of the other six SNPs (rs3764435, rs348471, rs63319, rs610529, rs7027604, rs8187876) were found to be associated with susceptibility to ATDILI. The findings first demonstrate that rs7852860 variants in ALDH1A1 gene is associated with susceptibility to ATDILI in the Chinese Han population. Validation studies with larger sample sizes and other ethnic groups are needed to confirm the findings.
Tris (1,3-dichloro-2-propyl) phosphate (TDCPP) has neurotoxicity, but its mechanism remains unclear. Evidence recently showed that ferroptosis might be associated with TDCPP-induced neurotoxicity. To ...explore the role and underlying mechanism of ferroptosis in TDCPP-induced neurotoxicity, the occurrence of ferroptosis was examined in mice and PC12 cells upon TDCPP exposure. The mechanism of TDCPP-induced ferroptosis was clarified in vitro combined with the RNA sequencing assay. The in vivo results showed that orally TDCPP exposure (100 mg/kg, 30 d) inhibited the learning and memory ability of mice, reduced hippocampus neurons, induced malondialdehyde (MDA) accumulation, and decreased glutathione (GSH) and superoxide dismutase (SOD) levels in the hippocampus. Moreover, TDCPP exposure (100 mg/kg, 30 d) altered the ferroptosis and autophagy-related protein abundances in the hippocampus. The in vitro results showed that TDCPP exposure (0, 5, 20, 50, 100, and 200 μM) for 24 h induced dose-dependent cell death in PC12 cells, and the cell death was ameliorated by the co-treatment with ferrostatin-1 (1 μM, 24 h). Similarly, TDCPP exposure (0, 50, 100, and 200 μM) for 24 h increased the levels of MDA and LPO, but decreased the reduced GSH in PC12 cells. Furthermore, TDCPP exposure (0, 50, 100, and 200 μM) for 24 h altered the ferroptosis and autophagy-related protein abundances in PC12 cells. The RNA-sequencing revealed that TDCPP exposure (100 μM, 24 h) induced mitophagy activation in SH-SY5Y cells. Meanwhile, the in vitro experiments confirmed that TDCPP exposure (0, 50, 100, and 200 μM) for 24 h increased abundances of mitophagy-related protein phosphatase and tensin homolog induced kinase 1(PINK1), Parkinson protein 2 E3 ubiquitin-protein ligase (PARKIN), inositol 1,4,5-trisphosphate receptor type 1 (IP3R1), and voltage-dependent anion channel 1 (VDAC1) in PC12 cells. Moreover, TDCPP treatment (100 μM, 24 h) increased the mitochondrial recruitment of PARKIN, decreased the mitochondrial membrane potential (MMP) level, and increased the Fe2+ level in mitochondria. In addition, decreased ATP levels and increased reactive oxygen species (ROS) levels were observed in PC12 cells upon TDCPP exposure (0, 50, 100, and 200 μM) for 24 h. In summary, ferroptosis was associated with TDCPP-induced neurotoxicity, and the mechanism might be related to PINK1/PARKIN-mediated mitophagy initiated by mitochondrial damage.
Organophosphorus flame retardant TDCPP induces neurotoxicity via mitophagy-related ferroptosis in vivo and in vitro (Created with BioRender.com). Display omitted
•Ferroptosis was associated with TDCPP-induced neurotoxicity.•TDCPP-induced ferroptosis might be related to PINK1/PARKIN-mediated mitophagy initiated by mitochondrial damage.•TDCPP induced mitochondrial depolarization via the VDAC channels activation.
•The structural parameters and relative content of key active functional groups changing law with oxygen concentration were analysed.•The changing characteristics of gas concentration with oxygen ...concentration were assessed.•The association between the key active groups and the coal spontaneous combustion index parameters under oxygen deprivation was determined.
Coal spontaneous combustion (CSC) has a devastating effect on the environment and human health. CSC primarily involves oxygen-lean oxidation and combustion states. In this study, to investigate the evolution of the coal microstructure during CSC in an oxygen-lean atmosphere, coal for oxygen-lean combustion was obtained and combusted at characteristic temperatures by using an independently developed electric tube furnace. Through Fourier-transform infrared spectroscopy, the relative contents of the active functional group of the initial-state oxidation coal were explored, and the main active functional groups, namely aromatic hydrocarbon, the oxygen functional group, aliphatic hydrocarbon, and the hydroxyl group, with the characteristic temperature, were determined. The sensitivities of different active functional groups to oxygen concentrations were analysed. In practice, a 10 vol% oxygen concentration was the key factor, inhibiting and promoting various active functional groups and exhibiting distinct dominance at various stages. Finally, the oxygen concentrations affected the gas concentration release characteristics, thereby determining the correlation degree of the key group and the oxygen concentration, as well as verifying the oxygen concentration sensitivity of the microstructure. The groups highly correlated with CSC characteristic parameters were mainly –CH2 and –CH3. The research results suggested remarkable explanatory potential to further elucidate the evolution of microstructures in oxygen-lean CSC.
As COVID-19 spread worldwide, many major grain-producing countries have adopted measures to restrict their grain exports; food security has aroused great concern from various parties. How to improve ...grain production has become one of the most important issues facing all countries. However, crop diseases are a difficult problem for many farmers so it is important to master the severity of crop diseases timely and accurately to help staff take further intervention measures to minimize plants being further infected. In this paper, a restructured residual dense network was proposed for tomato leaf disease identification; this hybrid deep learning model combines the advantages of deep residual networks and dense networks, which can reduce the number of training process parameters to improve calculation accuracy as well as enhance the flow of information and gradients. The original RDN model was first used in image super resolution, so we need to restructure the network architecture for classification tasks through adjusted input image features and hyper parameters. Experimental results show that this model can achieve a top-1 average identification accuracy of 95% on the Tomato test dataset in AI Challenger 2018 datasets, which verifies its satisfactory performance. The restructured residual dense network model can obtain significant improvements over most of the state-of-the-art models in crop leaf identification, as well as requiring less computation to achieve high performance.
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in ...high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent ...differentiation of ancient plants.
Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf.
We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.
Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ...ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S. octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203T and ex‐type: MUCL 58363; MycoBank no.: MB 847838).
The new fission yeast species Schizosaccharomyces lindneri is described. The description is based on data derived from phenotypic characterization, genomic sequence and structural analysis, and hybridization trials. Genomic rearrangements most likely played an important role during sympatric speciation. Strains of the new species were isolated from honeybee honey, which seems to be its main habitat. The new species is closely related to Schizosaccharomyces octosporus.
Take‐away
A new fission yeast species, Schizosaccharomyces lindneri sp. nov., is described.
The new species is closely related to Schizosaccharomyces octosporus. Delimitation of S. octosporus and S. lindneri sp. nov. is based on whole‐genome sequencing data and on hybridization trials.
An almost complete prezygotic and postzygotic sterility barrier was detected between S. octosporus and S. lindneri sp. nov.
Genome rearrangements most likely play an important role in hybrid infertility between S. octosporus and S. lindneri sp. nov. Most likely, speciation of S. lindneri was sympatric.
S. lindneri sp. nov. was isolated from honey bee honey.
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