ViMRT: a text-mining tool and search engine for automated virus mutation recognition.

MOTIVATION: Virus mutation is one of the most important research issues which plays a critical role in disease progression and has prompted substantial scientific publications. Mutation extraction from published literature has become an increasingly important task, benefiting many downstream applications such as vaccine design and drug usage. However, most existing approaches have low performances in extracting virus mutation due to both lack of precise virus mutation information and their development based on human gene mutations. RESULTS: We developed ViMRT, a text-mining tool and search engine for automated virus mutation recognition using natural language processing. ViMRT mainly developed 8 optimized rules and 12 regular expressions based on a development dataset comprising 830 papers of 5 human severe disease-related viruses. It achieved higher performance than other tools in a test dataset (1662 papers, 99.17% in F1-score) and has been applied well to two other viruses, influenza virus and severe acute respiratory syndrome coronavirus-2 (212 papers, 96.99% in F1-score). These results indicate that ViMRT is a high-performance method for the extraction of virus mutation from the biomedical literature. Besides, we present a search engine for researchers to quickly find and accurately search virus mutation-related information including virus genes and related diseases. AVAILABILITY AND IMPLEMENTATION: ViMRT software is freely available at http://bmtongji.cn:1225/mutation/index.

ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects.

Molecular mechanisms of virus-related diseases involve multiple factors, including viral mutation accumulation and integration of a viral genome into the host DNA. With increasing attention being paid to virus-mediated pathogenesis and the development of many useful technologies to identify virus mutations (VMs) and viral integration sites (VISs), much research on these topics is available in PubMed. However, knowledge of VMs and VISs is widely scattered in numerous published papers which lack standardization, integration and curation. To address these challenges, we built a pilot database of human disease-related Virus Mutations, Integration sites and Cis-effects (ViMIC), which specializes in three features: virus mutation sites, viral integration sites and target genes. In total, the ViMIC provides information on 31 712 VMs entries, 105 624 VISs, 16 310 viral target genes and 1 110 015 virus sequences of eight viruses in 77 human diseases obtained from the public domain. Furthermore, in ViMIC users are allowed to explore the cis-effects of virus-host interactions by surveying 78 histone modifications, binding of 1358 transcription regulators and chromatin accessibility on these VISs. We believe ViMIC will become a valuable resource for the virus research community. The database is available at http://bmtongji.cn/ViMIC/index.php.

Oriented Growth of Thin Films of Covalent Organic Frameworks with Large Single-Crystalline Domains on the Water Surface.

It has been a longstanding challenge to rationally synthesize thin films of organic two-dimensional (2D) crystals with large single-crystalline domains. Here, we present a general strategy for the creation of 2D crystals of covalent organic frameworks (COFs) on the water surface, assisted by a charged polymer. The morphology of the preorganized monomers underneath the charged polymer on the water surface and their diffusion were crucial for the formation of the organic 2D crystals. Thin films of 2D COFs with an average single-crystalline domain size of around 3.57 ± 2.57 µm2 have been achieved, and their lattice structure, molecular structure, and grain boundaries were identified with a resolution down to 3 Å. The swing of chain segments and lattice distortion were revealed as key factors in compensating for the misorientation between adjacent grains and facilitating error corrections at the grain boundaries, giving rise to larger single-crystalline domains. The generality of the synthesis method was further proved with three additional 2D COFs. The oriented single-crystalline domains and clear grain boundaries render the films as model materials to study the dependence of the vertical conductivity of organic 2D crystals on domain sizes and chemical structures, and significant grain boundary effects were illustrated. This study presents a breakthrough in the controlled synthesis of organic 2D crystals with structural control at the molecular level. We envisage that this work will inspire further investigation into the microstructure-intrinsic property correlation of 2D COFs and boost their application in electronics.

Nanoporous and Highly Thermal Conductive Thin Film of Single-Crystal Covalent Organic Frameworks Ribbons.

Nanoporous materials are widely explored as efficient adsorbents for the storage of gases and liquids as well as for effective low-dielectric materials in large-scale integrated circuits. These applications require fast heat transfer, while most nanoporous substances are thermal insulators. Here, the oriented growth of micrometer-sized single-crystal covalent organic frameworks (COFs) ribbons with nanoporous structures at an air-water interface is presented. The obtained COFs ribbons are interconnected into a continuous and purely crystalline thin film. Due to the robust connectivity among the COFs ribbons, the entire film can be easily transferred and reliably contacted with target supports. The measured thermal conductivity amounts to ∼5.31 ± 0.37 W m-1 K-1 at 305 K, which is so far the highest value for nanoporous materials. These findings provide a methodology to grow and assemble single-crystal COFs into large area ensembles for the exploration of functional properties and potentially lead to new devices with COFs thin films where both porosity and thermal conductivity are desired.

Dynamics of chloroplast proteome in salt-stressed mangrove Kandelia candel (L.) Druce.

Kandelia candel is being established as a model xylophyte for ecoadaptation due to its salt tolerance. To adapt to high salinity, the photosynthesis apparatus must function efficiently under these conditions. Proteomic analysis of chloroplasts isolated from plants under different degrees of salt stress was performed to quantify the changes of individual proteins and to gain a global view of the total chloroplast protein dynamics. Among the 1030 proteins quantified (unique peptide ≥ 1), 76 showed a more than 1.5-fold change in abundance, of which 36 are involved in the light-dependent reactions and 12 in the Calvin cycle. The dynamic change of these proteins indicates that light-dependent reactions are maintained by up-regulating the levels of component proteins at both moderate and high salinity, and the Calvin cycle remained functional at moderate salinity but showed a decline at high salinity. In addition to proteins related to photosynthesis, some known abiotic-stress proteins and plastoglobuli were up-regulated in salt-stressed plants. Plastoglobuli might contribute to maintaining membrane integrity and fluidity. In conclusion, this extensive proteomic investigation on intact chloroplasts of the salt-tolerant xylophyte under salt stress provides some important novel information on adaptative mechanisms involving photosynthesis in responses to salt stress in K. candel.

A knowledge empowered explainable gene ontology fingerprint approach to improve gene functional explication and prediction.

Functional explication of genes is of great scientific value. However, conventional methods have challenges for those genes that may affect biological processes but are not annotated in public databases. Here, we developed a novel explainable gene ontology fingerprint (XGOF) method to automatically produce knowledge networks on biomedical literature in a given field which quantitatively characterizes the association between genes and ontologies. XGOF provides systematic knowledge for the potential function of genes and ontologically compares similarities and discrepancies in different disease-XGOFs integrating omics data. More importantly, XGOF can not only help to infer major cellular components in a disease microenvironment but also reveal novel gene panels or functions for in-depth experimental research where few explicit connections to diseases have previously been described in the literature. The reliability of XGOF is validated in four application scenarios, indicating a unique perspective of integrating text and data mining, with the potential to accelerate scientific discovery.

Growth of single-crystal imine-linked covalent organic frameworks using amphiphilic amino-acid derivatives in water.

A core feature of covalent organic frameworks (COFs) is crystallinity, but current crystallization processes rely substantially on trial and error, chemical intuition and large-scale screening, which typically require harsh conditions and low levels of supersaturation, hampering the controlled synthesis of single-crystal COFs, particularly on large scales. Here we report a strategy to produce single-crystal imine-linked COFs in aqueous solutions under ambient conditions using amphiphilic amino-acid derivatives with long hydrophobic chains. We propose that these amphiphilic molecules self-assemble into micelles that serve as dynamic barriers to separate monomers in aqueous solution (nodes) and hydrophobic compartments of the micelles (linkers), thereby regulating the polymerization and crystallization processes. Disordered polyimines were obtained in the micelle, which were then converted into crystals in a step-by-step fashion. Five different three-dimensional COFs and a two-dimensional COF were obtained as single crystals on the gram scale, with yields of 92% and above.

Proteomic and physiological responses in mangrove Kandelia candel roots under short-term high-salinity stress.

Kandelia candel is one of the mangrove species that are most resistant to environmental stress. As a typical nonsalt-secreting mangrove plant, K. candel is an ideal biological material to analyze the molecular mechanism of salt tolerance in woody plants. In this study, changes in protein abundance and expression profile in K. candel roots under high-salinity stress of 600 mmol L-1 NaCl were analyzed using isobaric tags for relative and absolute quantification (iTRAQ) assay. Moreover, the physiological parameters associated with metabolic pathways in which the differentially abundant proteins (DAPs) are involved were determined. A total of 5577 proteins were identified by iTRAQ analysis of the K. candel root proteins, of which 227 were DAPs with a fold change ratio >1.2 or a fold change ratio <0.83 and a P-value <0.05. A total of 227 DAPs consisting of 110 up-regulated and 117 down-regulated proteins were identified. Our Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the DAPs were primarily involved in biological processes including carbohydrate and energy metabolisms, stress response and defense, cell wall structure, and secondary metabolism. The results of the physiological parameters showed that their profile changes were consistent with those of the proteome analysis. The results of the proteome and physiological parameters showed that K. candel roots could resist high-salinity stress by maintaining a normal Embden-Meyerhof-Parnas and tricarboxylic acid (EMP-TCA) pathway, increasing the activities of various antioxidant enzymes and antioxidant contents, stabilizing the cell wall structure, and accumulating secondary metabolites such as triterpenoids.

[Dynamic evaluation and driving forces of ecosystem services in Quanzhou bay estuary wetland, China]. / 泉州湾河口湿地生态系统服务价值的动态评价及驱动力分析.

Ecosystem service value (ESV) in 1997, 2005, 2013 and 2015 of Quanzhou Bay estuary wetland was evaluated dynamicly by market value, alternative value and opportunity cost methods, combined with classification of service indicators and deduplicate computing. The main driving forces for the changes of ESV and the pathway and intensity of their actions were identified using stepwise regression and path analysis methods. The results showed that the main ecosystem services of Quanzhou Bay estuary wetland were flood regulation, climate regulation, and food supply, which were directly driven by water supply, mariculture carrying capacity, and gross value of the regional production. Other drivers exerted indirect effect on the changes of main ESVs.

Palladium-Catalyzed Oxidative [2 + 2 + 1] Annulation of 1,7-Diynes with H2O: Entry to Furo[3,4- c]quinolin-4(5 H)-ones.

A novel cascade annulation of 1,7-diynes with water has been developed for the synthesis of furo[3,4- c]quinolin-4(5 H)-one skeletons with high atom- and step-economy. The transformation was enabled by a palladium catalyst in the presence of copper salt as the promoter, involving the formation of one C-C bond and two C-O bonds. Moreover, the reaction exhibits good tolerance of functional groups and broad substrate scope. Notably, the control experiments support the incorporation of the new oxygen atom from water.

Phosphoproteomics unveils stable energy supply as key to flooding tolerance in Kandelia candel.

The mangrove Kandelia candel (L.) Druce experiences daily flooding cycles. To explore the molecular mechanism underlying the physiological adaptation of K. candel to flooding, the potential role of protein phosphorylation in flooding responses was investigated by a large-scale quantitative phosphoproteomic analysis using isobaric tag for relative and absolute quantitation. Total 2141 unique phosphopeptides and 2603 non-redundant phosphorylation sites were identified from 1516 phosphoproteins in K. candel leaves. In addition to known phosphorylation motifs, three new motifs [GSP], [GxxSP] and [RSxS] were discovered. The phosphorylation levels of 96 differentially expressed phosphoproteins, including those involved in pyruvate metabolism and energy production, were identified in response to flooding. The physiological parameters and transcriptional levels relevant to flooding responses including photosynthesis, pyruvate metabolism, and ROS production were investigated and all were found to be robust under flooding conditions. The consistent results of the phosphoproteomic, physiological analyses and transcriptional levels reinforce each other to demonstrate that K. candel adapts to flooding through maintaining sufficient photosynthesis activities, achieving effective anaerobic respiration and increasing pentose phosphate pathway flux. Protein phosphorylation is likely to play a major role in the regulation of these pathways which together contribute to stable energy supply that enhances flooding tolerance in K. candel. BIOLOGICAL SIGNIFICANCE: Flooding stress is one of the major environmental stresses. The woody mangrove Kandelia candel experiences daily flooding cycles in its natural habitat. Protein phosphorylation is a crucial regulatory mechanism in plants' responses to both biotic and abiotic stresses. To analyze phosphorylation levels in critical enzymes involved in key metabolic pathways, we employed phosphoproteomic approach to dissect the adaptive mechanism of K. candel to flooding conditions. To our knowledge, this is the first large-scale quantitative phosphoproteomic analyses of K. candel's flooding responses. Multiplex iTRAQ-based quantitative proteomic and Nano-LC-MS/MS methods were used to construct the phosphorproteome. Our results indicate that K. candel is able to acquire stable energy supply under flooding by maintaining sufficient photosynthesis activities, enhancing effective anaerobic respiration and increasing pentose phosphate pathway (PPP) flux. The protein phosphorylation found in photosynthesis, anaerobic respiration and PPP is likely to play important roles in the flooding tolerance of K. candel.

Intermolecular cascade annulations of N-(arylsulfonyl)acrylamides with dual C(sp3)-H bonds: divergent access to indanes and pyrrolidin-2-ones.

A new divergent intermolecular cascade annulation reaction of N-(arylsulfonyl)acrylamides with dual alkyl C(sp3)-H bonds for producing two types of five-membered rings, indanes and pyrrolidin-2-ones, is described. By using cycloalkanes and common alkanes as a one-carbon unit, an intermolecular [4+1] cascade carboannulation of N-(arylsulfonyl)acrylamides was achieved via a sequence of three C-H bond functionalization/aryl migration/desulfonylation that enables the formation of three C-C bonds and one N-H bond. When the one-carbon unit was changed to cycloalkyl ethers, the alternative intermolecular [4+1] cascade heteroannulation reaction occurred and allowed the construction of two C-C bonds and one C-N bond through dual C-H bond functionalization, aryl migration and desulfonylation cascades.

Metal-Free Oxidative 1,2-Arylmethylation Cascades of N-(Arylsulfonyl)acrylamides Using Peroxides as the Methyl Resource.

A new, metal-free oxidative 1,2-arylmethylation cascades of N-(arylsulfonyl)acrylamides for the assembly of 2,2-disubstituted-N-arylbutanamides containing an all-carbon quaternary center is presented. This reaction enables the one-step formation of two new C-C bonds through a sequence of methylation/1,4-aryl migration/desulfonylation using an organic peroxide as the methyl resource with a broad substrate scope and excellent functional group tolerance.

Copper-catalyzed oxidative [2+2+1] annulation of 1,n-enynes with α-carbonyl alkyl bromides through C-Br/C-H functionalization.

The Cu-catalyzed oxidative [2+2+1] annulation of 1,n-enynes (n = 6, 7) with α-carbonyl alkyl bromides through C-Br/C-H functionalization has been developed. Using Ag2CO3/tert-butyl hydroperoxide (TBHP) as co-oxidants, α-carbonyl alkyl bromides provide two bonds, the α-C(sp(3))-Br bonds and the α-C(sp(3))-H bonds, to cyclize with the 1,n-enynes and Cu(MeCN)4PF6, thus forming three new C-C bonds and two rings in a single reaction.

Proteomic analysis of changes in the Kandelia candel chloroplast proteins reveals pathways associated with salt tolerance.

The plant chloroplast is one of the most sensitive organelles in response to salt stress. Chloroplast proteins extracted from seedling leaves were separated by two-dimensional gel electrophoresis (2-DE). More than 600 protein spots could be distinguished on each gel. Fifty-eight differentially expressed protein spots were detected, of which 46 could be identified through matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). These proteins were found to be involved in multiple aspects of chloroplast metabolism pathways such as photosynthesis, ATP synthesis, detoxification and antioxidation processes, nitrogen assimilation and fixation, protein metabolism, and tetrapyrrole biosynthesis. The results indicated that K. candel could withstand up to 500 mM NaCl stress for a measured period of 3 days, by maintaining normal or high photosynthetic electron transfer efficiency and an only slightly stimulated Calvin cycle. Meanwhile, we found that ROS scavenging, nitrogen assimilation, protein degradation and chaperone function in chloroplasts were also of importance for salt tolerance of K. candel. The ultrastructural and physiological data agree with chloroplast proteome results. These findings allow further exploration of our knowledge on salt adaptation in woody halophytes and may contribute to the development of more salt-tolerant plants in the future.

Proteomic analysis of salt-responsive proteins in the leaves of mangrove Kandelia candel during short-term stress.

Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na(+) compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H2O2) and superoxide anion radicals (O2(-)) contents, as well as Na(+) content and K(+)/Na(+) ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel.