Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis.

Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection.

Structural and electronic properties of α-, ß-, γ-, and 6,6,18-graphdiyne sheets and nanotubes.

α-, ß-, γ- and 6,6,18-graphdiyne (GDYs) sheets, as well as the corresponding nanotubes (GDYNTs) are investigated systematically by using the self-consistent-field crystal orbital method. The calculations show that the GDYs and GDYNTs with different structures have different electronic properties. The α-GDY sheet is a conductor, while 2D ß-, γ- and 6,6,18-GDYs are semiconductors. The carrier mobilities of ß- and γ-GDY sheets in different directions are almost the same, indicating the isotropic transport characteristics. In addition, the electron mobility is in the order of 106 cm2 V-1 s-1 and it is two orders of magnitude larger than the hole mobility of 2D γ-GDY. However, α- and 6,6,18-GDY sheets have anisotropic mobilities, which are different along different directions. For the 1D tubes, the order of stability is γ-GDYNTs > 6,6,18-GDYNTs > ß-GDYNTs > α-GDYNTs and is independent of the tube chirality and size. ß- and γ-GDYNTs as well as zigzag α- and 6,6,18-GDYNTs are semiconductors with direct bandgaps, while armchair α-GDYNTs are metals, and armchair 6,6,18-GDYNTs change from semiconductors to metals with increasing tube size. The armchair ß- and γ-GDYNTs are more favourable to transport holes, while the corresponding zigzag tubes prefer to transport electrons.

Identification of prognostic markers of lung cancer through bioinformatics analysis and in vitro experiments.

Lung cancer is one of the most common types of cancer worldwide. Understanding the molecular mechanisms underlying the development and progression of lung cancer may improve early diagnosis, treatment and prognosis. The aim of the present study was to examine the pathogenesis of lung cancer and to identify potentially novel biomarkers. Gene expression datasets of patients with lung cancer were obtained from the Gene Expression Omnibus. Genes which were most closely associated with lung cancer (core genes) were screened by weighted gene co­expression network analysis. In vitro cell based experiments were further utilized to verify the effects of the core genes on the proliferation of lung cancer cells, adhesion between cells and the matrix, and the associated metabolic pathways. Based on WGCNA screening, two gene modules and five core genes closely associated with lung cancer, including immunoglobulin superfamily member 10 (IGSF10) from the turquoise module, and ribonucleotide reductase regulatory subunit M2, protein regulator of cytokinesis 1, kinesin family member (KIF)14 and KIF2C from the brown module were identified as relevant. Survival analysis and differential gene expression analysis showed that there were significant differences in IGSF10 expression levels between the healthy controls and patients with lung cancer. In patients with lung cancer, IGSF10 expression was decreased, and the overall survival time of patients with lung cancer was significantly shortened. An MTT and colony formation assay showed that IGSF10­knockout significantly increased proliferation of lung cancer cells, and Transwell assays and adhesion experiments further suggested that the adhesion between cells and the matrix was significantly increased in IGSF10­knockout cells. Gene Set Enrichment Analysis showed that the expression level of IGSF10 was significantly associated with the activation of the integrin­ß1/focal adhesion kinase (FAK) pathway. Western blotting revealed that knockout of IGSF10 resulted in the activation of the integrin­ß1/FAK pathway, as the protein expression levels of integrin­ß1, phosphorylated (p)­FAK and p­AKT were significantly upregulated. Activation of the integrin­ß1/FAK pathway, following knockout of IGSF10, affected the proliferation and adhesion of lung cancer cells. Therefore, IGSF10 my serve as a potential prognostic marker of lung cancer.

Stabilities and electronic properties of nanowires made of single atomic sulfur chains encapsulated in zigzag carbon nanotubes.

Theoretical investigations are carried out on the recently synthesized one-dimensional nanowires made of atomic sulfur chains encapsulated in carbon nanotubes (called S@CNTs). Special attention is paid to stability, electronic property and transport properties of these combined nanowires. It is found that the encapsulation is exothermic when S@CNTs are built from the tubes with diameter larger than 6.4 Å. Thus the experimental results are energetically favorable since the diameters of the CNTs are about 6 Å in the obtained S@CNTs. The combined nanowires can be stabilized by van der Waals interaction between sulfur chain and tube as indicated from radial distribution function and reduced density gradient descriptions. All S@CNTs studied in this work exhibit metallic property with the partially filled bands. However, the conducting component and the pathway of charge carriers are various. For instance, only the sulfur chain is the conducting pathway for S@CNT(8, 0), while both the sulfur chain and tube are the conducting pathways for S@CNT(9, 0). This interesting feature was understood based on the band structures and crystal orbital analysis. The electronic transport properties of the systems are performed by investigating and analyzing the transmission spectra, current-voltage (I-V) curves and transmission eigenstate, which confirm that the sulfur chains can improve the electronic transport of CNTs. Moreover, the electrostatic interaction resulted from the charge transfer between the two components of S@CNTs should be favorable to the stability of the combined nanowires.

Electronic Property Modulation of One-Dimensional Extended Graphdiyne Nanowires from a First-Principle Crystal Orbital View.

Graphdiyne and derivatives with delocalized π-electron systems are of particular interest owing to their structural, electronic, and transport properties, which are important for potential applications in next-generation electronics. Inspired by recently obtained extended graphdiyne nanowires, explorations of the modulation of the band gap and carrier mobility of this new species are still needed before application in device fabrication. To provide a deeper understanding of these issues, herein we present theoretical studies of one-dimensional extended graphdiyne nanowires using first-principle calculations. Modulation of the electronic properties of the extended graphdiyne nanowire was investigated systemically by considering several chemical and physical factors, including electric field, chemical functionalization, and carbo-merization. The band gap was observed to increase upon application of an electric field parallel to the plane of the synthesized graphdiyne nanowire in a non-periodic direction. Although chemical functionalization and carbo-merization caused the band gaps to decrease, the semiconducting property of the nanowires was preserved. Band gap engineering of the extended graphdiyne nanowires was explored regarding the field strength and the number of -C≡C- units in the carbon chain fragments. The charge carrier mobility of chemically functionalized and carbo-merized extended graphdiyne nanowires was also calculated to provide a comparison with pristine nanowire. Moreover, crystal orbital analysis was performed in order to discern the electronic and charge transport properties of the extended graphdiyne nanowires modified by the aforementioned chemical and physical factors.

Crystal orbital studies on the 1D silic-diyne nanoribbons and nanotubes.

This work presents crystal orbital studies on novel one-dimensional (1D) nanoscale materials derived from a Si-diyne sheet, based on the density functional theory. The two-dimensional (2D) Si-diyne layer is observed to be carbo-merized silicene, with a similar structure to graphdiyne. The 2D Si-diyne and its 1D ribbons and tubes, of different size and chirality, have been addressed systematically. The low dimensional Si-diyne materials studied exhibit relatively high stability, according to phonon-frequency calculations and molecular dynamics simulations. With comparable diameters, the Si-diyne tubes have lower strain energies than silicene and silicon carbide nanotubes. The Si-diyne layer and its 1D derivatives are all semiconductors, regardless of the size and chirality of the strips and tubes. In addition, the band gaps of the 1D Si-diyne nanoribbons and nanotubes with different chirality, always monotonically decrease as their sizes increases. A quantitative relationship between the band gap and the size of the ribbons and tubes was obtained. The mobility of charge carriers for the 1D Si-diyne structures was also investigated. It was found that both hole and electron mobility of the ribbons and tubes exhibit linear increase with increasing size. The electrons have greater mobility than the holes for each strip and tube. In addition, the mechanical properties of the Si-diyne nanostructures were also investigated by calculation of the Young's modulus and the Poisson's ratio.

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Structure and electronic properties of the double-wall nanotubes constructed from SiO2 nanotubes encapsulated inside zigzag carbon nanotubes.

This paper presents ab initio self-consistent field crystal orbital calculations on the structures, stabilities, elastic and electronic properties of the double-wall nanotubes made of SiO(2) nanotubes encapsulated inside zigzag carbon nanotubes based on density functional theory. It is found that formation of the combined systems is energetically favorable when the nearest distance between the two constituents is in the area of the van der Waals effect. The obtained band structures show that all the combined systems are semiconductors with nonzero energy gaps. Based on the deformation potential theory and effective mass approximation, the mobilities of charge carriers are calculated to be in the range of 10(2)-10(4) cm(2) V(-1) s(-1), the same order of magnitude as those of the corresponding zigzag carbon nanotubes. The Young's moduli are also calculated for the combined systems.

The magnetic coupling in manganese-based dinuclear superhalogens and their analogues. A theoretical characterization from a combined DFT and BS study.

The structures, relative stabilities, vertical detachment energies and magnetic coupling properties of a series of manganese-based dinuclear superhalogens and their isoelectronic analogues are explored via a combined density functional theory and broken symmetry study. Both the capabilities of various exchange-correlation functionals and basis set effects are investigated. The large magnitudes of the calculated exchange coupling constants indicate clearly the apparent molecular magnetism of these new types of superhalogen. Encouragingly, the high possibility of the coexistence of both high stability and strong magnetic coupling in these new polynuclear superhalogens is also confirmed. Besides these, the larger magnitudes of the calculated coupling constants of iron-based clusters here, compared with the homodinuclear [Mn(2)Cl(5)](-) cluster, demonstrate the possibility of the existence of strong magnetic coupling in potential iron-based homo- and heterodinuclear superhalogens. The analysis of spin density distribution is also performed in order to understand the coupling mechanisms.

Combined DFT and BS study on the exchange coupling of dinuclear sandwich-type POM: comparison of different functionals and reliability of structure modeling.

The exchange coupling of a group of three dinuclear sandwich-type polyoxomolybdates [MM'(AsMo7O27)2](12-) with MM' = CrCr, FeFe, FeCr are theoretically predicted from combined DFT and broken-symmetry (BS) approach. Eight different XC functionals are utilized to calculate the exchange-coupling constant J from both the full crystalline structures and model structures of smaller size. The comparison between theoretical values and accurate experimental results supports the applicability of DFT-BS method in this new type of sandwich-type dinuclear polyoxomolybdates. However, a careful choice of functionals is necessary to achieve the desired accuracy. The encouraging results obtained from calculations on model structures highlight the great potential of application of structure modeling in theoretical study of POM. Structural modeling may not only reduce the computational cost of large POM species but also be able to take into account the external field effect arising from solvent molecules in solution or counterions in crystal.

Theoretical study on the peanut-shaped dimers and nanotubes consisted of C50 cages.

The structures and electronic properties of the peanut-shaped dimers and nanotubes consisted of C50 cages are investigated based on the ab initio self-consistent field molecular and crystal orbital calculations. It is found that the formation of peanut-shaped dimers is energeticlly favorable. The corresponding peanut-shaped nanotubes are semiconductors due to existence of the energy gaps. These peanut-shaped nanotubes are predicted to have smaller Young moduli than the single-walled carbon nanotube. The anionic peanut-shaped nanotubes are also calculated in this paper, as well as the infrared spectra of the peanut-shaped dimers.

Combined DFT and NBO study on the electronic basis of Si...N-beta-donor bond.

Two groups of isoelectronic molecules with different SiXN (X=C, N, O ) units are analyzed by a combined DFT and NBO study to investigate the electronic basis of Si...N-beta-donor bond. The influence of various energy components on the formation of Si...N-beta-donor bond is explored. The importance of the electron delocalization from the lone pair of nitrogen atom into the acceptor-orbitals connected with Si atom is elicited by our calculations. The electron delocalization from the lone pair of nitrogen atom into the antibonding orbital of Si-X bond is quite different among the isoelectronic molecules with various types of SiXN units.

Octacoordinate carbons encaged inside carborane clusters: a density functional theory investigation.

This work focuses on the computational design and characterization of a novel series of endohedral carborane clusters containing octacoordinate carbon centers. The structural and bonding features and the thermodynamic and kinetic stabilities are discussed extensively based on density functional theory calculations. These nonclassical carboranes are fascinating in structure not only for the octacoordinate carbon center but also for the surrounding carbon and boron ligands with inverted bonding configuration. These endohedral carboranes are higher in energy than the corresponding exohedral isomers due to the high strain in the system. A new stability rule based on the donor-acceptor model is proposed to predict the stability ordering for these carborane isomers. In addition, some of these octacoordinate carboranes might have relatively high kinetic stabilities, which is rather hopeful for the experimental syntheses.

Bonding analysis and stability on alternant B16N16 cage and its dimers.

Bonding analysis is performed on alternant B(16)N(16) cage based on a combined study of DFT with NBO method. The main feature of such analysis is the separation of bonding structure into two components: sigma skeleton and pi bond system. Each component is further decomposed into contributions from various NBOs, thus we obtain the details of bonding interactions of every BN unit. Based on these results, relative stability of four covalent dimers of B(16)N(16) is predicted and this prediction is verified by DFT calculations. So the possibility of forecasting properties of oligomers just from analysis on monomer is highlighted in this way.

Hexa- and octacoordinate carbon in hydrocarbon cages: theoretical design and characterization.

A new series of hydrocarbon cages containing hexa- and octacoordinate carbon centers were designed theoretically by performing DFT calculations at the B3 LYP/6-311+G** level. Among these non-classical structures that were found to still obey the 8e rule, the two tetracations with octacoordinate carbons may be the first examples found in pure hydrocarbons. Structural characteristics, as well as thermodynamic and kinetic stabilities, were also investigated theoretically for these two octacoordinate tetracations. These hydrocarbon compounds containing hypercoordinate carbon centers provide a challenge for synthetic organic chemists.

Structures and electronic properties of peanut-shaped dimers and carbon nanotubes.

The structures and electronic properties of peanut-shaped dimers and carbon nanotubes constructed from C60 molecules are investigated using ab initio self-consistent field molecular and crystal orbital methods based on the density-functional theory. The calculations show that the formation of peanut-shaped structures without octagonal carbon rings is energetically favorable. The obtained band structures indicate that the peanut-shaped nanotube can be a semiconductor or a metal.

7-trifluoromethylquinoline-functionalized luminescent photochromic spiropyran with the stable merocyanine species both in solution and in the solid state.

A new spiropyran (SP2) with the stable merocyanine form (MC2) both in solution and in the solid state at room temperature was designed and synthesized. The stability of MC2 is believed to be due to the electron-withdrawing effect of both the quinoline and the trifluoromethyl groups. (1)H NMR spectra indicate that the ratio of the open form vs the closed form of SP2 is dependent on the polarity of solvents. Single crystals composed of only the open form (MC2) were successfully obtained. X-ray structural analysis indicates that except trifluoromethyl and two methyl groups MC2 is completely planar with an s-trans,s-cis conformation. It should be noted that this is the first report of the X-ray crystal structure of the pure open form of spiropyran. MC2 can be slowly transformed into SP2 at -30 degrees C or lower temperature, and the process is accelerated by visible light irradiation. This special photochromic behavior can be explained by the calculated thermodynamic data. The spectral properties of SP2/MC2 in the presence of different metal ions are also studied, and the results show the potential application of SP2/MC2 in sensing metal ions.

1D silver(I) complex of nitronyl nitroxide with strong spin-spin interaction through silver(I) ion.

A 1D silver(I) complex of nitronyl nitroxide was prepared and its structure was determined by X-ray diffraction analysis; magnetic studies indicate that the spin-spin interaction of nitronyl nitroxides through silver(I) ions along the chain are fairly strong (J/kb = -84 K).