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.

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.

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.

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.

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.

Characteristic profiles of biofilm, enterotoxins and virulence of Staphylococcus aureus isolates from dairy cows in Xinjiang Province, China.

As an important zoonotic pathogen, Staphylococcus aureus has led to serious mastitis and endometritis in infected dairy cows. In this study, a total of 164 strains of S. aureus were isolated from dairy cows in Xinjiang Province, China, and subjected to assays to determine drug susceptibility and biofilm (BF) formation ability. Enterotoxin-related genes were detected, and the transcription levels of genes related to BF formation were determined by using reverse transcription-quantitative polymerase chain reaction. Moreover, the pathogenicity of isolates with different BF formation abilities was determined by measuring their hemolysis activity, half lethal dose (LD50) and organ bacterial load. The results showed that 86.0% of S. aureus isolates could form BF. Among them, 42.1% of the strains had weak BF formation ability, and most strains with a strong BF formation ability were ica gene carriers. The S. aureus isolates displayed multidrug resistance and their drug resistance was positively correlated with their BF formation ability. Moreover, 96.3% of the S. aureus isolates carried enterotoxin genes. Among them, the detection rates of the novel enterotoxin genes were higher than those of conventional enterotoxin genes. Furthermore, isolates with a strong BF formation ability had higher LD50 but lower hemolysis ability and organ bacterial load than those of the isolates with weak or no BF ability. However, isolates without BF ability produced more severe pathological changes than those of isolates with strong BF formation ability. These findings suggest that higher BF ability and presence of novel enterotoxin genes are important characteristics of S. aureus isolates from dairy cows in Xinjiang Province, China, and such isolates may pose potential threats to food safety.

Regulation of magnetic relaxation behavior by replacing 3d transition metal ions in [M2Dy2] complexes containing two different organic chelating ligands.

Four tetranuclear 3d-4f complexes, namely [Fe2Ln2(L)2(teaH)2(Cl)2](NO3)2·4CH3CN (H2L = N1,N3-bis(3-methoxysalicylidene)diethylenetriamine, teaH3 = triethanolamine, Ln = Dy for 1 and Ln = Gd for 1') and [Co2Ln2(L)2(pdm)2(CH3COO)2(CH3OH)2](NO3)2·xCH3OH·yH2O (pdmH2 = 2,6-pyridinedimethanol, Ln = Dy, x = 5 and y = 2.5 for 2 and Ln = Gd, x = 6 and y = 1.5 for 2'), have been reported. Two FeIII and two DyIII in 1 formed a zigzag Fe1-Dy1-Dy1a-Fe1a arrangement with a Fe1-Dy1-Dy1a angle of 105.328(3)°. However, in contrast to 1, two CoIII and two DyIII ions in 2 formed a more linear Co1-Dy1-Dy1a-Co1a arrangement with a Co1-Dy1-Dy1a angle of 141.86(2)°. Additionally, two DyIII ions in 1 are eight-coordinated with a triangular dodecahedron geometry, while two DyIII ions in 2 adopt nine-coordination with a muffin geometry. Magnetic studies revealed slow magnetic relaxation behavior for 1, with an energy barrier Ea of 6.9 K. For 2, single molecule magnet behavior was presented under a zero dc field with an effective energy barrier Ueff of 64.0(9) K. Ab initio calculations for 1 and 2 indicate that compared to 2, complex 1 has a larger transversal magnetic moment of its ground Kramers doublets (KD) and a larger value of the tunnelling parameter (Δt) for the exchanged coupled ground state, which may result in poor single molecule magnet behavior for 1.

Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi.

The false spider mite Brevipalpus yothersi infests a broad host plant range and has become one of the most economically important species within the genus Brevipalpus. This phytophagous mite inflicts damage by both feeding on plants and transmitting plant viruses. Here, we report the first draft genome sequence of the false spider mite, which is also the first plant virus mite vector to be sequenced. The ∼72 Mb genome (sequenced at 42× coverage) encodes ∼16,000 predicted protein-coding genes.

Single molecule magnet behaviors of Zn4Ln2 (Ln = DyIII, TbIII) complexes with multidentate organic ligands formed by absorption of CO2 in air through in situ reactions.

In this work, we report the syntheses, crystal structures and magnetic properties of three novel Zn-Ln mixed metal complexes, namely [Zn4Dy2(L1)2(L2)2(N3)2]Cl2·2H2O (1), [Zn4Tb2(L1)2(L2)2(Cl)2][ZnN3Cl3]·2H2O (2), and [Zn4Gd2(L1)2(L2)2(Cl)2][ZnN3Cl3]·2H2O (3), in which L12- and L23- were formed from the ligand L [L = N1,N3-bis(3-methoxysalicylidene)diethylenetriamine] through in situ reactions. Interestingly, carbon dioxide in air was absorbed in the process of forming carbamate ligand L23-; this can be ascribed to the insertion of CO2 into M-N amide bonds. Moreover, 1 and 2 represent the first series of 3d-4f SMMs containing carbamate ligands by fixation of CO2 in air. Single-crystal X-ray diffraction analyses reveal that the crystal structures of 1 and 2 are anion-dependent, i.e., the apical positions of the two ZnII ions in 1 and 2 are occupied by an N atom of N3- and by Cl-, respectively. However, the topologies of 2 and 3 are similar. Two ZnII ions and one LnIII (Ln = Dy (1), Tb (2) and Gd (3)) form nearly linear trinuclear [Zn2Ln] units which are double-bridged by two L23- ligands. Magnetic studies reveal that two complexes show single molecule magnet behavior under a direct current (dc) field, with effective energy barriers (Ueff) of 30.66(5) K for 1 and 8.87(3) K for 2. Ab initio calculations reveal that the DyIII ions in 1 and the TbIII ions in 2 are axial in nature; however, a difference in the tunnel splitting of 1 and 2 leads to variation in the magnetization blockades of the two complexes. Theoretical calculations also indicate that the directions of the main magnetic axes severely deviate from the coordination atoms of the first spheres of DyIII and TbIII in 1 and 2; thus further results in poor SMM behavior of the two complexes.

Amino-nitramino functionalized triazolotriazines: a good balance between high energy and low sensitivity.

Using a simple and efficient approach, a series of fused triazolo-triazine compounds, namely, 2,5-dinitramide-7-amino-[1,2,4]triazolo[1,5-a][1,3,5]triazine (2) and its energetic salts (4-9, 11-13), were prepared by nitration of 2,5,7-triamine [1,2,4]triazolo[1,5-a][1,3,5]triazine (1) with 100% nitric acid, followed by reacting with the corresponding bases. All new compounds were comprehensively characterized. Structures of 2 and 4 were further confirmed by single crystal X-ray diffraction. Based on the measured densities and calculated heats of formation (Gaussian 09), detonation pressures and velocities were evaluated by EXPLO5, falling in the range of 21.5-34.2 GPa and 7823-9313 m s-1, respectively. Notably, impact and friction tests show that these compounds are very insensitive (IS > 40 J; FS > 360 N). Moreover, two representative compounds 5 and 6 with high decomposition temperature (5: 194 °C; 6: 199 °C), excellent detonation properties (vD = 9313, 9088 m s-1; P = 33.9, 34.1 GPa) as well as rarely low sensitivities (IS > 40 J; FS > 360 N) are promising candidates as high-energy and insensitive explosives.

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.

Bandgap engineering of a lead-free defect perovskite Cs3Bi2I9 through trivalent doping of Ru3.

Inorganic defect halide compounds such as Cs3Bi2I9 have been regarded as promising alternatives to overcome the instability and toxicity issues of conventional perovskite solar cells. However, their wide indirect bandgaps and deep defect states severely limit their photoelectronic conversion efficiency when implemented in devices. Trivalent cation substitution has been proposed by previous calculations allowing the engineering of their band structures, but experimental evidences are still lacking. Herein we use the trivalent cation Ru3+ to partially replace Bi3+ in Cs3Bi2I9, and reveal their structural and optoelectronic properties, as well as the environmental stability. The Ru-doped Cs3Bi2I9 shows a decreasing bandgap with the increasing doping levels and an overall up-shift of band structure, owing to the dopant-induced defect states and thus enhanced phonon-electron coupling. As a result, upon Ru3+ doping, the narrowed bandgap and the upward shift of the band structures might facilitate and broaden their applications in optoelectronic devices.

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.

Thermally controlling the singlet-triplet energy gap of a diradical in the solid state.

Diradicals, molecules with two unpaired electrons, are reactive intermediates that play an important role in many fields. Their defining feature is the energy difference between their singlet and triplet states, which provides direct information on the extent of their electron exchange interactions. Such knowledge is essential for understanding their diradical character, which is controllable internally by modification of the electronic and steric properties of the substituents. We now report that the energy gap of a diradical in the solid state can also be controlled by an external stimulus. The dication diradical of 4,4''-di(bisphenylamino)-p-terphenyl exhibits two singlet states with different exchange coupling constants at different temperatures as determined by SQUID and EPR measurements. The behavior is induced by the conformation change of the terphenyl bridge, the key structural unit of the species. The work presents an unprecedented instance of a thermally controllable singlet-triplet gap for a crystalline diradical and provides a novel diradical material relevant to the design of functional materials.

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.

Single-Chain Magnets Based on Octacyanotungstate with the Highest Energy Barriers for Cyanide Compounds.

By introducing large counter cations as the spacer, two isolated 3, 3-ladder compounds, (Ph4P)[Co(II)(3-Mepy)2.7(H2O)0.3W(V)(CN)8] · 0.6H2O (1) and (Ph4As)[Co(II)(3-Mepy)3W(V)(CN)8] (2, 3-Mepy = 3-methylpyridine), were synthesized and characterized. Static and dynamic magnetic characterizations reveal that compounds 1 and 2 both behave as the single-chain magnets (SCMs) with very high energy barriers: 252(9) K for 1 and 224(7) K for 2, respectively. These two compounds display the highest relaxation barriers for cyano-bridged SCMs and are preceded only by two cobalt(II)-radical compounds among all SCMs. Meanwhile, a large coercive field of 26.2 kOe (1) and 22.6 kOe (2) were observed at 1.8 K.