Recent Advances in Various Metal-Organic Channels for Photochemistry beyond Confined Spaces.

Tailor-made molecular channel architectures are a hot issue in the fields of nanotechnology, molecular sieves, ion sensors, recognition, confined space reactors, and fluidic transport systems. Carbon nanotubes have been a particular focus, though they cannot easily be synthesized to predefined structures and sizes. Rational design and construction of molecular channel structures based on coordination chemistry has been recognized as a useful approach. Metal-organic channel (MOC) structures can be generated by utilizing, at least in principle, molecular self-assembly of metal ions as angular units with designed ligands as spacers. Recent developments in molecular channel chemistry include exciting advances in photochemical applications and supramolecular material functionality, in addition to general applications such as transport, diffusion and exchange, separation, gas storage, catalysis, and simple encapsulation. In order to carry out the diverse channel functionalities, a large number of studies have been conducted on the synthesis of robust and stable 3D coordination polymers, which show permanent porosity without any guest molecules within the channels, in that the robustness of the channel structures after removal of the solvate/guest molecules is of interest because the structural integrity of the extended structures must be maintained during the reactions. These compounds can be regarded as analogous to zeolites. This Account highlights advances in the construction, from metal cations and multidentate pyridyl ligands, of various MOCs and useful molecular materials as photoreaction platforms. We begin by discussing the fact that detailed proof-of-concept construction of various systematic MOC structures has been introduced mainly in terms of the metal ions as angular components and the pyridyl ligands as spacers. This approach leads to structural complexity of assembled MOC motifs such as metallamacrocycles, helical and cylindrical coordination polymers, vertical arrays of 1D coordination polymers, interweaving and eclipsed stacking of 2D coordination polymers, and typical 3D coordination polymers. Notwithstanding the diversity of their skeletal structures, confined spaces of the channels are suitable for the study of photochemical performances including radical trapping, photocyclopropanation, dye inclusion and energy transfer, and guest-to-host structural transmission. The key aspect of their utility is not only the preparation of photoresistant MOCs but also channel tuning for inclusion of photoactive guests. Guest molecules, which are compatible with the size, shape, and polarity of the channels, can be incorporated into the crystals, instead of simple organic solvents, thus giving rise to host-guest complexes in the solid state. Such MOC studies could facilitate the development of chemical sensors, new photocatalytic systems, and useful molecular photochemical reactors.

Antibacterial activities of viriditoxin congeners and synthetic analogues against fish pathogens.

Viriditoxin is a fungal secondary metabolite of the fungus Paecilomyces variotii derived from the inner tissues of the giant jellyfish Nemopilema nomurai. Viriditoxin exhibits antibacterial activity against Streptococcus iniae and Streptococcus parauberis, which are major pathogens of aqua cultured fish. Viriditoxin induced abnormal cell morphologies in the fish pathogens S. iniae and S. parauberis, presumably by inhibiting FtsZ polymerization as was previously observed in Escherichia coli. Synthetic analogues of viriditoxin, designed based on docking simulation results to FtsZ of Staphylococcus aureus, were prepared and compared with viriditoxin for antibacterial activity. Reconstitution of free hydroxyl or carboxyl groups of the methoxyl or methyl ester groups of viriditoxin led to significant reduction of antibacterial activity, implying that the natural molecule is optimized for antibacterial activity to deter bacteria potentially harmful to Paecilomyces.

A Novel Peroxisome Proliferator-activated Receptor (PPAR)γ Agonist 2-Hydroxyethyl 5-chloro-4,5-didehydrojasmonate Exerts Anti-Inflammatory Effects in Colitis.

Inflammatory bowel disease (IBD) is a chronic inflammatory disease with increasing incidence and prevalence worldwide. Here we investigated the newly synthesized jasmonate analogue 2-hydroxyethyl 5-chloro-4,5-didehydrojasmonate (J11-Cl) for its anti-inflammatory effects on intestinal inflammation. First, to test whether J11-Cl can activate peroxisome proliferator-activated receptors (PPARs), we performed docking simulations because J11-Cl has a structural similarity with anti-inflammatory 15-deoxy-Δ(12,14)-prostaglandin J2 (15d-PGJ2), one of the endogenous ligands of PPARγ. J11-Cl bound to the ligand binding domain of PPARγ in the same manner as 15d-PGJ2 and rosiglitazone, and significantly increased transcriptional activity of PPARγ. In animal experiments, colitis was significantly reduced in mice with J11-Cl treatment, determined by analyses of survival rate, body weight changes, clinical symptoms, and histological evaluation. Moreover, J11-Cl decreased production of pro-inflammatory cytokines including IL-6, IL-8, and G-CSF as well as chemokines including chemokine (C-C motif) ligand (CCL)20, chemokine (C-X-C motif) ligand (CXCL)2, CXCL3, and chemokine (C-X3-C motif) ligand 1 (CX3CL1) in colon tissues, and LPS or TNF-α-stimulated macrophages and epithelial cells. In contrast, production of anti-inflammatory cytokines including IL-2 and IL-4 as well as the proliferative factor, GM-CSF, was increased by J11-Cl. Furthermore, inhibition of MAPKs and NF-κB activation by J11-Cl was also observed. J11-Cl reduced intestinal inflammation by increasing the transcriptional activity of PPARγ and modulating inflammatory signaling pathways. Therefore, our study suggests that J11-Cl may serve as a novel therapeutic agent against IBD.

Pyramiding of two rice bacterial blight resistance genes, Xa3 and Xa4, and a closely linked cold-tolerance QTL on chromosome 11.

KEY MESSAGE: We fine mapped the Xa4 locus and developed a pyramided rice line containing Xa3 and Xa4 R - alleles and a cold-tolerance QTL. This line will be valuable in rice breeding. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease of cultivated rice. Pyramiding BB resistance genes is an essential approach for increasing the resistance level of rice varieties. We selected an advanced backcross recombinant inbred line 132 (ABL132) from the BC3F7 population derived from a cross between cultivars Junam and IR72 by K3a inoculation and constructed the mapping population (BC4F6) to locate the Xa4 locus. The Xa4 locus was found to be delimited within a 60-kb interval between InDel markers InDel1 and InDel2 and tightly linked with the Xa3 gene on chromosome 11. After cold (4 °C) treatment, ABL132 with introgressions of IR72 in chromosome 11 showed lower survival rate, chlorophyll content, and relative water content compared to Junam. Genetic analysis showed that the cold stress-related quantitative trait locus (QTL) qCT11 was located in a 1.3-Mb interval close to the Xa4 locus. One line, ABL132-36, containing the Xa3 resistance allele from Junam, the Xa4 resistance allele from IR72, and the cold-tolerance QTL from Junam (qCT11), was developed from a BC4F6 population of 250 plants. This is the first report on the pyramiding of Xa3 and Xa4 genes with a cold-tolerance QTL. This region could provide a potential tool for improving resistance against BB and low-temperature stress in rice-breeding programs.

Synthesis and antibacterial evaluation of hamacanthin B analogues.

Hamacanthins are a class of antibacterial bisindole alkaloids isolated from marine sponges. Based on structure-activity relationships and in silico MRSA PK binding analysis of these bisindole alkaloids, the authors designed new hamacanthin B derivatives and evaluated their antibacterial activities against drug-resistant pathogens. Racemates of the synthetic products were resolved into their enantiomers by chiral separation using a cellulose column, and antibacterial activities were compared. Unsaturation of the central heterocyclic ring structure and bromine substitution at the indole moiety were found to enhance the antibacterial activities of hamacanthin B analogues.

Synthesis of Phthalimide Derivatives as Potential PPAR-γ Ligands.

Paecilocin A, a phthalide derivative isolated from the jellyfish-derived fungus Paecilomyces variotii, activates PPAR-γ (Peroxisome proliferator-activated receptor gamma) in rat liver Ac2F cells. Based on a SAR (Structure-activity relationships) study and in silico analysis of paecilocin A-mimetic derivatives, additional N-substituted phthalimide derivatives were synthesized and evaluated for PPAR-γ agonistic activity in both murine liver Ac2F cells and in human liver HepG2 cells by luciferase assay, and for adipogenic activity in 3T3-L1 cells. Docking simulation indicated PD6 was likely to bind most strongly to the ligand binding domain of PPAR-γ by establishing crucial H-bonds with key amino acid residues. However, in in vitro assays, PD1 and PD2 consistently displayed significant PPAR-γ activation in Ac2F and HepG2 cells, and adipogenic activity in 3T3-L1 preadipocytes.

Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight (BB) in rice (Oryza sativa L.). In this study, we investigated the genome-wide transcription patterns of two Xoo strains (KACC10331 and HB1009), which showed different virulence patterns against eight rice cultivars, including IRBB21 (carrying Xa21). In total, 743 genes showed a significant change (p-value < 0.001 in t-tests) in their mRNA expression levels in the HB1009 (K3a race) strain compared with the Xoo KACC10331 strain (K1 race). Among them, four remarkably enriched GO terms, DNA binding, transposition, cellular nitrogen compound metabolic process, and cellular macromolecule metabolic process, were identified in the upregulated genes. In addition, the expression of 44 genes was considerably higher (log2 fold changes > 2) in the HB1009 (K3a race) strain than in the Xoo KACC10331 (K1 race) strain. Furthermore, 13 and 12 genes involved in hypersensitive response and pathogenicity (hrp) and two-component regulatory systems (TCSs), respectively, were upregulated in the HB1009 (K3a race) strain compared with the Xoo KACC10331 (K1 race) strain, which we determined using either quantitative real-time PCR analysis or next-generation RNA sequencing. These results will be helpful to improve our understanding of Xoo and to gain a better insight into the Xoo-rice interactions.

Construction of Hetero-Four-Layered Tripalladium(II) Cyclophanes by Transannular π⋠⋠⋠π Interactions.

A synthetic strategy for the generation of new molecular species utilizing a provision of nature is presented. Nano-dimensional (23(2)×21(1)×16(1) ų) hetero-four-layered trimetallacyclophanes were constructed by proof-of-concept experiments that utilize a suitable combination of π⋅⋅⋅π interactions between the central aromatic rings, tailor-made short/long spacer tridentate donors, and the combined helicity. The behavior of the unprecedented four-layered metallacyclophane system offers a landmark in the development of new molecular systems.

Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.).

KEY MESSAGE: A new bacterial blight resistance gene has been identified through fine-mapping, which confers high levels of resistance to all Korean Xanthomonas oryzae pv. oryzae (Xoo) races, including the new Xoo race K3a. Rice bacterial leaf blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious constraint to rice production in Asia and Africa. The japonica advanced backcross breeding lines derived from the indica line IR65482-7-216-1-2 in the background of cultivar Junam are resistant to all Korean BB races, including K3a. To identify the gene(s) involved in resistance to Korean Xoo races, the association of genotypic and phenotypic variations was examined in two F2 populations derived from the crosses between 11325 (IR83261-3-7-23-6-2-1-1-2-1-2)/Anmi and 11325/Ilpum. The segregation ratios of F2 individuals from the crosses of 11325/Anmi and 11325/Ilpum were 578 resistant:209 susceptible and 555 resistant:241 susceptible, respectively, which is consistent with the expected allelic frequency of a 3:1 ratio. Genetic analysis using graphical mapping indicated that resistance (R) was controlled by a new resistance gene linked with the flanking markers RM27320 and ID55.WA18-5 within an approximately 80-kb region between 28.14 and 28.22 Mbp on chromosome 11. The eight candidate genes functionally predicted were included in the target region. Examination of the candidate genes by RT-PCR analysis only corroborated with the significant difference in transcript levels of the WAK3 gene in the presence or absence of pathogen infection. Allelism tests performed with other known BB R-genes revealed that the allele was distinct from others having a similar chromosomal location.

Organization and Energy Transfer of Fused Aromatic Hydrocarbon Guests within Anion-Confining Nanochannel MOFs.

The self-assembly of Zn(II) ions with 1,3,5-tris(isonicotinoyloxyethyl)cyanurate produces new topological (4(2)⋅12(4))3(4(3))4 2D metal-organic frameworks (MOFs) with anion-confining cages. The eclipsed assembly of each 2D MOF by π-π stacking of cyanurate moieties (3.352(5) Å) forms 3D MOFs consisting of nanochannels (10.5 Å). Two of the three anions are confined in each peanut-type cage, resulting in hydrophobicity of the nanochannels. The hydrophobic nanochannel effectively adsorbs a wide range of fused aromatic hydrocarbons (FAHs) as monomers or dimers, rendering it potentially highly useful as an energy-transfer material.

Solvent media as the driving force in the formation of one-dimensional silver(I) coordination polymers with 2-methylidene-1,3-bis(nicotinoyloxy)propane.

Two kinds of silver(I) coordination polymers consisting of the same chemical composition, [Ag(CF3SO3)(L)] [L is 2-methylidene-1,3-bis(nicotinoyloxy)propane], were synthesized and characterized by infrared (IR) and photoluminescence (PL) spectroscopy, elemental and thermal analyses, and single-crystal X-ray diffractometry; these are catena-poly[[(trifluoromethanesulfonato-κO)silver(I)]-µ-2-methylenepropane-1,3-diyl dinicotinate-κ2N:N'], [Ag(CF3SO3)(C16H14N2O4)]n, and its chloroform monosolvate, {[Ag(CF3SO3)(C16H14N2O4)]·CHCl3}n. The X-ray crystallographic measurements revealed that the silver(I) compounds exhibit one-dimensional sinusoidal or helical molecular structures depending on the solvent used for crystallization. Self-assembly in a methanol/chloroform mixture produces the sinusoidal molecular strand, whereas recrystallization from acetonitrile medium affords a racemic mixture of the helical strands. These compounds display a fluorescence emission arising from both the ligand-centred transition and the ligand-to-metal charge transfer (LMCT) in the solid state under ambient conditions.

Motion of an isolated water molecule within a flexible coordination cage: structural properties and catalytic effects of ionic palladium(II) complexes.

The unique cage complexes [[(Me(4)en)Pd](3)(L)(2)](X)(6) (L = 1,3,5-tris(isonicotinoyloxyethyl)cyanurate; X(-) = BF(4)(-), ClO(4)(-)) were constructed. A single water molecule in a skeletal cage was reversibly associated and dissociated via a combination of the adequate space, polar environment, and conformational flexibility of the cage. In Suzuki-Miyaura C-C cross-coupling reactions, the cage complex showed significant catalytic activity along with the effects of the isolated single water molecule.

Cyclodimers versus cyclotrimers via solvent or temperature effects on metallacyclization.

The reaction of (COD)PdCl 2 (COD = 1,5-cyclooctadiene) with bis(3-pyridyl)methylphenylsilane (L) in acetone affords single crystals consisting of cyclodimers, [PdCl 2(L)] 2, whereas the reaction in a mixture of dichloromethane and ethanol yields amorphous spheres consisting of cyclotrimers, [PdCl 2(L)] 3. The interconversion and morphology control between the crystals and the microspheres can be explained by the difference in flexibility between the cyclodimer and cyclotrimer.

Novel ß-phenylacrylic acid derivatives exert anti-cancer activity by inducing Src-mediated apoptosis in wild-type KRAS colon cancer.

Many stress conditions including chemotherapy treatment is known to activate Src and under certain condition Src can induce the apoptotic signal via c-Jun N-terminal kinase (JNK) activation. Here we report that the newly synthesized ß-phenylacrylic acid derivatives, MHY791 and MHY1036 (MHYs), bind to epidermal growth factor receptor (EGFR) tyrosine kinase domains and function as EGFR inhibitors, having anti-cancer activities selectively in wild-type KRAS colon cancer. Mechanistically, MHYs-induced Src/JNK activation which enhanced their pro-apoptotic effects and therefore inhibition of Src by the chemical inhibitor PP2 or Src siRNA abolished the response. In addition, MHYs generated reactive oxygen species and increased ER stress, and pretreatment with antioxidant-inhibited MHY-induced ER stress, Src activation, and apoptosis. Furthermore, the irreversible EGFR inhibitor PD168393 also activated Src while the reversible EGFR inhibitor gefitinib showed the opposite effect, indicating that MHYs are the irreversible EGFR inhibitor. Collectively, Src can play a key role in apoptosis induced by the novel EGFR inhibitor MHYs, suggesting that activation of Src might prove effective in treating EGFR/wild-type KRAS colon cancer.

Analysis of virulence and growth of a purine auxotrophic mutant of Xanthomonas oryzae pathovar oryzae.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice. A random insertional mutant library of Xoo KACC10331 was constructed using a Tn5-derived transposon, and the virulence of the mutants against the susceptible rice cultivar IR24 was assayed. After the virulence assay, the M793 (purD::Tn5) mutant that had reduced virulence against the rice plants was isolated. Thermal asymmetric interlaced-PCR and sequence analysis revealed that the transposon was inserted into the purD gene (encodes a phosphoribosylamine-glycine ligase) of the M793 mutant. The reverse transcriptase-PCR assay revealed that the mutation of the purD gene did not affect the expression of other purine biosynthesis genes. However, the M793 mutant required exogenous purines and thiamine for growth in minimal media. These results indicate that the purD gene plays a crucial role in the growth and virulence of Xoo.

Recyclable scavengers for photo-cyclopropanation via an in situ crystallization process.

The palladium(ii) cyclophane systems, constructed by previously reported proof-of-concept self-assembly, represent a crucial landmark in the field of effective and recyclable scavenging of triiodide (I3-) in the photo-cyclopropanation of alkenes with CH2I2. The scavenger's driving force behind photo-cyclopropanation is the efficient in situ crystallization of triiodide-exchanged species. The exact quantitative photoreaction yields according to the mole ratios of the cyclophane system are impressive. The recycling behavior can be ascribed to the rigidity and stability of the four-layered tripalladium(ii)cyclophane.

Photoreaction of adsorbed diiodomethane: halide effects of a series of neutral palladium(ii) coordination cages.

A series of Pd6L4-type neutral coordination cages, [Pd6X12L4] (X(-) = Cl(-) and Br(-)), are constructed via self-assembly of (COD)PdCl2 and K2PdBr4 with C3-symmetric N,N',N''-tris(2-pyridinylmethyl)-1,3,5-benzenetricarboxamide (L), respectively. The iodide analogue [Pd6I12L4] is smoothly synthesized from [Pd6Br12L4] in the presence of CH2I2 under mild conditions. The replacement of bromide to iodide in the nanocage system represents a landmark achievement in synthetic-methodology development. The CH2I2 molecules are adsorbed in the order [Pd6I12L4] > [Pd6Br12L4] > [Pd6Cl12L4] and in the "like-attracts-like" pattern, presumably owing to the van der Waals force. Irradiation of [Pd6I12L4]·3.5CH2I2 with 1-methylcyclohexene in chloroform at 350 nm preferentially affords the cyclopropanation product.

A triple-function nanotube as a reactant reservoir, reaction platform, and byproduct scavenger for photo-cyclopropanation.

Herein, we report the advanced-concept triple-functionality of a metal-organic nanotube (MONT), which acts as a reservoir for unstable reactants, a photoreaction platform, and a scavenger for byproduct iodine. Self-assembly of CdI2 with a new Y-type ligand (L) produces the substantial 1D MOF, [CdI2(L)], thus forming a thick nanotube with a 1.4 nm diameter.

Simultaneous Detection of Three Bacterial Seed-Borne Diseases in Rice Using Multiplex Polymerase Chain Reaction.

Burkholderia glumae (bacterial grain rot), Xanthomonas oryzae pv. oryzae (bacterial leaf blight), and Acidovorax avenae subsp. avenae (bacterial brown stripe) are major seedborne pathogens of rice. Based on the 16S and 23S rDNA sequences for A. avenae subsp. avenae and B. glumae, and transposase A gene sequence for X. oryzae pv. oryzae, three sets of primers had been designed to produce 402 bp for B. glumae, 490 bp for X. oryzae, and 290 bp for A. avenae subsp. avenae with the 63°C as an optimum annealing temperature. Samples collected from naturally infected fields were detected with two bacteria, B. glumae and A. avenae subsp. avenae but X. oryzae pv. oryzae was not detected. This assay can be used to identify pathogens directly from infected seeds, and will be an effective tool for the identification of the three pathogens in rice plants.