ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics.

Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https://ngdc.cncb.ac.cn/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.

TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies.

Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes and traits, are now leading to a better understanding of the complex mechanisms of genetic variants in regulating various diseases and traits. Despite the ever-increasing TWAS outputs, there is still a lack of databases curating massive public TWAS information and knowledge. To fill this gap, here we present TWAS Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase of TWAS findings manually curated from extensive literature. In the current implementation, TWAS Atlas collects 401,266 high-quality human gene-trait associations from 200 publications, covering 22,247 genes and 257 traits across 135 tissue types. In particular, an interactive knowledge graph of the collected gene-trait associations is constructed together with single nucleotide polymorphism (SNP)-gene associations to build up comprehensive regulatory networks at multi-omics levels. In addition, TWAS Atlas, as a user-friendly web interface, efficiently enables users to browse, search and download all association information, relevant research metadata and annotation information of interest. Taken together, TWAS Atlas is of great value for promoting the utility and availability of TWAS results in explaining the complex genetic basis as well as providing new insights for human health and disease research.

TSomVar: a tumor-only somatic and germline variant identification method with random forest.

Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.

CancerSCEM: a database of single-cell expression map across various human cancers.

With the proliferating studies of human cancers by single-cell RNA sequencing technique (scRNA-seq), cellular heterogeneity, immune landscape and pathogenesis within diverse cancers have been uncovered successively. The exponential explosion of massive cancer scRNA-seq datasets in the past decade are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment of various cancer types. To fill this gap, we developed a database of Cancer Single-cell Expression Map (CancerSCEM, https://ngdc.cncb.ac.cn/cancerscem), particularly focusing on a variety of human cancers. To date, CancerSCE version 1.0 consists of 208 cancer samples across 28 studies and 20 human cancer types. A series of uniformly and multiscale analyses for each sample were performed, including accurate cell type annotation, functional gene expressions, cell interaction network, survival analysis and etc. Plus, we visualized CancerSCEM as a user-friendly web interface for users to browse, search, online analyze and download all the metadata as well as analytical results. More importantly and unprecedentedly, the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates seven analyze functions, where investigators can interactively perform cancer scRNA-seq analyses. In all, CancerSCEM paves an informative and practical way to facilitate human cancer studies, and also provides insights into clinical therapy assessments.

PADS Arsenal: a database of prokaryotic defense systems related genes.

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types of defense systems have been discovered, but there is no comprehensive defense systems database to organize prokaryotic defense gene datasets. To fill this gap, we unveil the prokaryotic antiviral defense system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public database dedicated to gathering, storing, analyzing and visualizing prokaryotic defense gene datasets. The initial version of PADS Arsenal integrates 18 distinctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 genomes across 33 390 species of archaea and bacteria. PADS Arsenal provides various ways to retrieve defense systems related genes information and visualize them with multifarious function modes. Moreover, an online analysis pipeline is integrated into PADS Arsenal to facilitate annotation and evolutionary analysis of defense genes. PADS Arsenal can also visualize the dynamic variation information of defense genes from pan-genome analysis. Overall, PADS Arsenal is a state-of-the-art open comprehensive resource to accelerate the research of prokaryotic defense systems.

Influence of the Different Types of Auxiliary Noncarboxylate Organic Ligands on the Topologies and Magnetic Relaxation Behavior of Zn-Dy Heterometallic Single Molecule Magnets.

In this work, we first synthesized a Zn-Dy complex, [Zn6Dy2(L)6(tea)2(CH3OH)2]·6CH3OH·8H2O (H2L = N-3-methoxysalicylidene-2-amino-3-hydroxypyridine, teaH3 = triethanolamine, 1), by employing H2L, anhydrous ZnCl2, and Dy(NO3)3·5H2O reacting with auxiliary ligand teaH3 in the mixture of CH3OH and DMF. When teaH3 and the solvent CH3OH in the reaction system of 1 were replaced by the auxiliary ligand 2,6-pyridinedimethanol (pdmH2) and the solvent MeCN, another Zn-Dy complex, [Zn4Dy4(L)6(pdm)2(pdmH)4]·10CH3CN·5H2O (2), was obtained. For 1, its crystal structure can be viewed as a dimer of two Zn3DyIII units. However, for 2, four DyIII form a zigzag arrangement, and each of its terminals linked two ZnII ions. Interestingly, although the structural topologies of 1 and 2 are different, the coordination geometries of DyIII in 1 and 2 are all triangular dodecahedron (TDD-8). The difference is that the continuous shape measure (CShM) values of DyIII in 1 are larger than the corresponding values in 2. Magnetic investigation revealed that the diluted sample 1@Y exhibits two magnetic relaxation processes, while 2 only exhibits a single relaxation process. Ab initio calculations indicated that, in the crystal lattice of 1, two complexes exhibiting slightly different CShM values of DyIII result in the double relaxation behavior of 1@Y. However, for 2, one of two DyIII fragments possesses a fast quantum tunneling of magnetization (QTM), resulting in its magnetic process presented at T < 1.8 K, so 2 exhibits single relaxation behavior. More importantly, the theoretical calculations also clearly indicated that the weak ligation at equatorial sites of DyIII in 1 and 2 ensure 1@Y and 2 possess SMM behavior, although the coordination geometry of DyIII (TDD-8) in 1 and 2 severely deviates from the ideal polyhedron and its axial symmetry is low.

Melatonin: A Multifunctional Factor in Plants.

Melatonin (N-acetyl-5-methoxy-tryptamine) is a universal molecule that is present in animals and plants. It has been detected in different kinds of plants and organs in different levels. Melatonin in plants shares the same initial biosynthesis compound with auxin, and therefore functions as indole-3-acetic acid like hormones. Moreover, melatonin is involved in regulating plant growth and development, protecting plants against biotic and abiotic stresses, such as salt, drought, cold, heat and heavy metal stresses. Melatonin improves the stress tolerance of plants via a direct pathway, which scavenges reactive oxygen species directly, and indirect pathways, such as increasing antioxidate enzymes activity, photosynthetic efficiency and metabolites content. In addition, melatonin plays a role in regulating gene expression, and hence affects performance of plants. In this review, the biosynthesis pathway, growth and development regulation, and the environment stress response of melatonin in plants are summarized and future research directions and priorities of melatonin in plants are speculated.

An Isolable Diboron-Centered Diradical with a Triplet Ground State.

Two new diboranes, 2,6-bis(BMes2 )mesitylene (1) and 3,3'-bis(BMes2 )bimesitylene (3), were synthesized. Two-electron reduction of 1 with elemental potassium afforded the C-H activation product [(18-c-6)K(THF)2 ]2+ ⋅22- bearing a BC3 four-membered ring as colorless crystals, whereas the reduction of 3 with potassium led to the isolation of [(18-c-6)K(THF)2 ]2+ ⋅32-.. as dark blue crystals. Both reduction products were characterized by structural and spectroscopic methods. Electron paramagnetic resonance (EPR) spectroscopy and theoretical calculations revealed that the electron spin density of 32-.. mainly resides on the two boron nuclei and features a triplet ground state, which was confirmed by superconducting quantum interference device (SQUID) measurements as well as theoretical calculations. 32-.. represents the first structurally characterized boron-centered diradical with a triplet ground state. In addition, the reactivity of [(18-c-6)K(THF)2 ]2+ ⋅32-.. toward PhSeSePh and nBu3 SnH was investigated, which is consistent with its radical character.

Elusive Antimony-Centered Radical Cations: Isolation, Characterization, Crystal Structures, and Reactivity Studies.

One-electron oxidation of the stibines Aryl3 Sb (1, Aryl=2,6-i Pr2 -4-OMe-C6 H2 ; 2, Aryl=2,4,6-i Pr3 -C6 H2 ) with AgSbF6 and NaBArylF4 (ArylF =3,5-(CF3 )2 C6 H3 ) afforded the first structurally characterized examples of antimony-centered radical cations 1.+ [BArylF4 ]- and 2.+ [BArylF4 ]- . Their molecular and electronic structures were investigated by single-crystal X-ray diffraction, electron paramagnetic resonance spectroscopy (EPR) and UV/Vis absorption spectroscopy, in conjunction with theoretical calculations. Moreover, their reactivity was investigated. The reaction of 2.+ [BArylF4 ]- and p-benzoquinone afforded a dinuclear antimony dication salt 32+ [BArylF4 ]2- , which was characterized by NMR spectroscopy and X-ray diffraction analysis. The formation of the dication 32+ further confirms that the isolated stibine radical cations are antimony-centered.

Magnetic Bistability in a Discrete Organic Radical.

Molecular assembly with magnetic bistability has been of considerable interest for application as electronic devices. In contrast to transition-metal complexes, magnetic bistability so far observed in organic radical crystals is mainly caused by intermolecular electron-exchange interaction. We now report that the magnetic bistability in an organic radical can also be caused by intramolecular electron-exchange interaction. The diradical salt of 1,4-di(bisphenylamino)-2,3,5,6,-tetramethylbenzene undergoes a phase transition with a thermal hysteresis loop over the temperature range from 118 to 131 K. The phases above and below the loop correspond to two different singlet states of the diradical dication. The results provide a novel organic radical material as an unprecedented instance of an intramolecular magnetic bistability revalent to the design of functional materials.

An Aliphatic Solvent-Soluble Lithium Salt of the Perhalogenated Weakly Coordinating Anion [Al(OC(CCl3)(CF3)2)4](-).

The facile synthesis of a new highly aliphatic solvent-soluble Li(+) salt of the perhalogenated weakly coordinating anion [Al(OC(CCl3)(CF3)2)4](-) and its application in stabilizing the Ph3C(+) cation were investigated. The lithium salt Li[Al(OC(CCl3)(CF3)2)4] (4) was prepared by the treatment of 4 mol equiv of HOC(CCl3)(CF3)2 with purified LiAlH4 in n-hexane from -20 °C to room temperature. Compound 4 is highly soluble in both polar and nonpolar solvents, and it bears both CCl3 and CF3 groups, resulting in a lower symmetry around the Al center compared to that of Li[Al(OC(CF3)3)4] (1). Treatment of 4 with Ph3CCl afforded the ionic compound [Ph3C][Al(OC(CCl3)(CF3)2)4] (5) bearing the Ph3C(+) cation with concomitant elimination of LiCl, suggesting the potential application of [Al(OC(CCl3)(CF3)2)4](-) in stabilizing reactive cationic species. Compounds 4 and 5 were fully characterized by spectroscopic and structural methods.

Electrochemical Synthesis and Magnetic Properties of [Cu9W6]: The Ultimate Member of the Quindecanuclear Octacyanometallate-Based Transition-Metal Cluster?

[Cu9W6], synthesized by the electrochemical method, may be the ultimate member of the quindecanuclear octacyanometallate-based transition-metal cluster. Its single-crystal structure and magnetic properties were characterized.

Access to Stable Metalloradical Cations with Unsupported and Isomeric Metal-Metal Hemi-Bonds.

Metalloradical species [Co2 Fv(CO)4 ](.+) (1(.+) , Fv=fulvalenediyl) and [Co2 Cp2 (CO)4 ](.+) (2(.+) , Cp=η(5) -C5 H5 ), formed by one-electron oxidations of piano-stool cobalt carbonyl complexes, can be stabilized with weakly coordinating polyfluoroaluminate anions in the solid state. They feature a supported and an unsupported (i.e. unbridged) cobalt-cobalt three-electron σ bond, respectively, each with a formal bond order of 0.5 (hemi-bond). When Cp is replaced by bulkier Cp* (Cp*=η(5) -C5 Me5 ), an interchange between an unsupported radical [Co2 Cp*2 (CO)4 ](.+) (anti-3(.+) ) and a supported radical [Co2 Cp*2 (µ-CO)2 (CO)2 ](.+) (trans-3(.+) ) is observed in solution, which cocrystallize and exist in the crystal phase. 2(.+) and anti-3(.+) are the first stable thus isolable examples that feature an unsupported metal-metal hemi-bond, and the coexistence of anti-3(.+) and trans-3(.+) in one crystal is unprecedented in the field of dinuclear metalloradical chemistry. The work suggests that more stable metalloradicals of metal-metal hemi-bonds may be accessible by using metal carbonyls together with large and weakly coordinating polyfluoroaluminate anions.

Tuning ground states of bis(triarylamine) dications: from a closed-shell singlet to a diradicaloid with an excited triplet state.

Three bis(triarylamine) dications were isolated by using weakly coordinating anions. Their electronic structures in the ground state were investigated by various experiments in conjunction with theoretical calculations. The ground-state electronic structures of these species were tunable by substituent effects, with two of them as closed-shell singlets and one of them as an open-shell singlet in the solid state. The excited state of the latter is thermally accessible, indicated by EPR and SQUID measurements. The work provides a new and stable diradicaloid structure motif with an excited triplet sate.

Rapid detection of Akabane virus by a novel reverse transcription loop-mediated isothermal amplification assay (RT-LAMP).

BACKGROUND: Akabane disease, caused by Akabane virus, is an insect-transmitted disease of ruminants that is primarily characterized by fetal damage. METHODS AND RESULTS: In this study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of Akabane virus was successfully developed. The primers were designed to target the highly conserved fragment of nucleoprotein from the Akabane virus. The results indicate that the assay is highly specific and sensitive with a detection limit of 5.0 TCID50/mL within a 60-min incubation time. A total of 126 abortive samples collected from Xinjiang province were detected by the established RT-LAMP. The results of RT-LAMP assay showed 96.8% agreement with the semi-nested RT-PCR. CONCLUSION: This study is to first to develop a rapid, sensitive, and accurate method for the detection of Akabane virus, which may be used to screen clinical samples in developing countries or regions.

RsbV of Listeria monocytogenes contributes to regulation of environmental stress and virulence.

SigmaB factor is an important regulatory factor for stress response in Gram-positive bacteria such as Listeria monocytogenes (L. monocytogenes), Staphylococcus aureus and Bacillus subtilis. However, the activity of SigmaB factor is regulated by RsbV factor. Currently, the functional studies of RsbV factor are mostly focused on non-pathogenic B. subtilis, but the roles of RsbV factor in pathogenic L. monocytogenes during the regulation of environmental stress and virulence are still unclear. In the study, a ∆RsbV mutant of L. monocytogenes was constructed to explore the regulatory role of RsbV in environmental stress and virulence. The environmental stress experiments indicated that the growth and survival capability of ∆RsbV mutant obviously decreased in stress of low temperature, osmotic pressure, alcohol and acid, compared with EGD strain. The macrophage infection experiment indicated that ∆RsbV mutant had weaker survival capability than EGD strain, and the expression of PrfA, actA, PlcA and LLO was down-regulated in infected cells. Animal inoculation experiments indicated that RsbV deletion significantly reduced the pathogenicity of L. monocytogenes. Our data demonstrate that, in addition to regulating tolerance under environmental stress conditions, RsbV also contributes to regulation of L. monocytogenes virulence.

[Effects of the deletion of RsbV gene on virulence of Listeria monocytogenes].

OBJECTIVE: To study the effect of RsbV gene deletion on the virulence of Listeria monocytogenes. METHODS: The fragment with RsbV deletion was generated by gene overlap extension PCR (SOE-PCR) and the mutant with RsbV deletion was obtained by homologous recombination based on the wild strain LM-XS5. The differences in virulence between the two strains were determined by LD50, bacterial counts in liver and spleen, and qRT-PCR experiments. RESULTS: LD50 of the RsbV gene-deleted strain was 10(4) higher than that of the wild strain. The numbers of gene-deleted strain in the mouse's liver and spleen were significantly fewer than that of the wild strain (P < 0.05). Results of qRT-PCR show that four virulence factors' expression levels of the RsbV gene-deleted strain were significantly lower than that of the wild strain (P < 0.05). The RsbV gene-deleted strain induced a strong immune response in mice against the wild strain. CONCLUSION: RsbV regulates the expression of four virulence gene (inlA, LLO, PlcA and PrfA) of Listeria monocytogenes; The virulence of the RsbV gene-deleted strain is significantly reduced, but it still has good immunogenicity.

Single molecule magnet behavior and luminescence of {Ln4} and {LnZn} complexes.

A series of tetranuclear coordination clusters [Ln4L2(HL)2(µ3-OH)2(NO3)2](NO3)2 [Ln = Dy (1·3CH3CN·5H2O), Gd (2·4CH3CN·5H2O), H2L = 6,6'-dimethoxy-2,2'-[2,2-dimethylpropane-1,3-diylbis-(nitrilomethylidyne)] diphenol] and dinuclear complexes [LnZnL(NO3)3(H2O)]·2CH3CN [Ln = Dy (3), Er (4), Yb (5), Lu (6)] were prepared and characterized. Static magnetic measurements revealed the presence of ferromagnetic interactions between the Dy(III) ions and weak antiferromagnetic couplings between the Gd(III) ions in 1 and 2. Dynamic magnetic studies showed that complexes 1 and 3 exhibit slow magnetic relaxation under a zero static field as expected for single molecule magnet (SMM) behavior, whereas complex 4 is a field-induced SMM. Clear hysteresis loops were observed for 1 and 3 at 2 K, verifying their SMM behavior. Luminescence investigations demonstrated that complexes 1 and 2 show ligand-based emission and can act as luminescence thermometers below 100 K, whereas complexes 3 and 5 display the characteristic emission of lanthanide ions. From the high-resolution emission spectra of 3 and 5, the energy gaps between the ground state and excited states of Dy(III) and Yb(III) ions were determined.

Eicosanuclear cluster [Cu(13)W(7)] of copper-octacyanotungstate bimetallic assembly: synthesis, structure, and magnetic properties.

Octacyanotungstate(V) reacts with Cu(NO(3))(2).2H(2)O and 1,4,7-trimethyl-1,4,7-triazacyclononane in methanol, resulting in an eicosanuclear cluster [Cu(13)W(7)], which shows a diamondoid shape with a Tolkowsky cut and bears intracluster ferromagnetic coupling.

(H(3)O)Nd(SO(4))(2).

The crystal structure of oxonium neodymium bis(sulfate), (H(3)O)Nd(SO(4))(2), shows a two-dimensional layered framework assembled from SO(4) tetrahedra and NdO(9) tricapped trigonal prisms. One independent sulfate group makes four S-O-Nd linkages, while the other makes five such connections to generate an unprecedented anhydrous anionic [Nd(SO(4))(2)](-) layer. To achieve charge balance, H(3)O(+) cations are inserted between adjacent layers where they participate in hydrogen-bonding interactions with the sulfate O atoms of adjacent layers.