Probing Interfacial Electronic Effects on Single-Molecule Adsorption Geometry and Electron Transport at Atomically Flat Surfaces.

Clarifying interfacial electronic effects on molecular adsorption is significant in many chemical and biochemical processes. Here, we used STM breaking junction and shell-isolated nanoparticle-enhanced Raman spectroscopy to probe electron transport and adsorption geometries of 4,4'-bipyridine (4,4'-BPY) at Au(111). Modifying the surface with 1-butyl-3-methylimidazolium cation-containing ionic liquids (ILs) decreases surface electron density and stabilizes a vertical orientation of pyridine through nitrogen atom σ-bond interactions, resulting in uniform adsorption configurations for forming molecular junctions. Modulation from vertical, tilted, to flat, is achieved on adding water to ILs, leading to a new peak ascribed to CC stretching of adsorbed pyridyl ring and 316 % modulation of single-molecule conductance. The dihedral angle between adsorbed pyridyl ring and surface decreases with increasing surface electronic density, enhancing electron donation from surface to pyridyl ring.

Research and Application of Several Key Techniques in Hyperspectral Image Preprocessing.

This paper focuses on image segmentation, image correction and spatial-spectral dimensional denoising of images in hyperspectral image preprocessing to improve the classification accuracy of hyperspectral images. Firstly, the images were filtered and segmented by using spectral angle and principal component analysis, and the segmented results are intersected and then used to mask the hyperspectral images. Hyperspectral images with a excellent segmentation result was obtained. Secondly, the standard reflectance plates with reflectance of 2 and 98% were used as a priori spectral information for image correction of samples with known true spectral information. The mean square error between the corrected and calibrated spectra is less than 0.0001. Comparing with the black-and-white correction method, the classification model constructed based on this method has higher classification accuracy. Finally, the convolution kernel of the one-dimensional Savitzky-Golay (SG) filter was extended into a two-dimensional convolution kernel to perform joint spatial-spectral dimensional filtering (TSG) on the hyperspectral images. The SG filter (m = 7,n = 3) and TSG filter (m = 3,n = 4) were applied to the hyperspectral image of Pavia University and the quality of the hyperspectral image was evaluated. It was found that the TSG filter retained most of the original features while the noise information of the filtered hyperspectral image was less. The hyperspectral images of sample 1-1 and sample 1-2 were processed by the image segmentation and image correction methods proposed in this paper. Then the classification models based on SG filtering and TSG filtering hyperspectral images were constructed, respectively. The results showed that the TSG filter-based model had higher classification accuracy and the classification accuracy is more than 98%.

A Hydrolase-Catalyzed Cyclization Forms the Fused Bicyclic ß-Lactone in Vibralactone.

Vibralactone is isolated from the basidiomycete fungus Boreostereum vibrans as one of the strongest lipase inhibitors. Its unusual ß-lactone-fused bicycle is derived from an aryl ring moiety by an oxidative ring-expansion prior to an intramolecular cyclization. Herein, we report the discovery of the cyclase VibC which belongs to the α/ß-hydrolase superfamily and is involved in the vibralactone biosynthesis. Biochemical and crystal studies suggest that VibC may catalyze an aldol or an electrocyclic reaction initiated by the Ser-His-Asp catalytic triad. For the aldol and pericyclic chemistry in living cells, VibC is a unique hydrolase performing the carbocycle formation of an oxepinone to a fused bicyclic ß-lactone. This presents a naturally occurring, new enzymatic reaction in both aldol and hydrolase (bio)chemistry that will guide future exploitation of these enzymes in synthetic biology for chemical-diversity expansion of natural products.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

Rapid discovery and functional characterization of diterpene synthases from basidiomycete fungi by genome mining.

Basidiomycete fungi are a rich source of bioactive diterpenoid secondary metabolites. However, compared with the large number of diterpene synthases (di-TPSs) identified in plants and ascomycete fungi, only three di-TPSs have been described from basidiomycete fungi. Large scale genome sequencing projects combined with the development of synthetic biology techniques now has enabled the rapidly discovery and characterization of di-TPSs from basidiomycete fungi. In this study, we discovered and functionally characterized four di-TPSs from 220 genome sequenced basidiomycete fungi by a combined strategy of genomic data mining, phylogenetic analysis and fast products characterization with synthetic biology techniques. Among them, SteTC1 of Stereum histurum was characterized as the first fungal cembrane diterpene synthase; PunTC of Punctularia strigosozonata and SerTC of Serpula lacrymans were characterized as ent-kauran-16α-ol synthase and DenTC3 of Dentipellis sp was characterized as a cyathane synthase. Our results provide opportunities for the discovery of new diterpenoids from basidiomycete fungi by genome mining.

Genome-wide analysis of ionotropic receptor gene repertoire in Lepidoptera with an emphasis on its functions of Helicoverpa armigera.

The functions of the Ionotropic Receptor (IR) family have been well studied in Drosophila melanogaster, but only limited information is available in Lepidoptera. Here, we conducted a large-scale genome-wide analysis of the IR gene repertoire in 13 moths and 16 butterflies. Combining a homology-based approach and manual efforts, totally 996 IR candidates are identified including 31 pseudogenes and 825 full-length sequences, representing the most current comprehensive annotation in lepidopteran species. The phylogeny, expression and sequence characteristics classify Lepidoptera IRs into three sub-families: antennal IRs (A-IRs), divergent IRs (D-IRs) and Lepidoptera-specific IRs (LS-IRs), which is distinct from the case of Drosophila IRs. In comparison to LS-IRs and D-IRs, A-IRs members share a higher degree of protein identity and are distinguished into 16 orthologous groups in the phylogeny, showing conservation of gene structure. Analysis of selective forces on 27 orthologous groups reveals that these lepidopteran IRs have evolved under strong purifying selection (dN/dS≪1). Most notably, lineage-specific gene duplications that contribute primarily to gene number variations across Lepidoptera not only exist in D-IRs, but are present in the two other sub-families including members of IR41a, 76b, 87a, 100a and 100b. Expression profiling analysis reveals that over 80% (21/26) of Helicoverpa armigera A-IRs are expressed more highly in antennae of adults or larvae than other tissues, consistent with its proposed function in olfaction. However, some are also detected in taste organs like proboscises and legs. These results suggest that some A-IRs in H. armigera likely bear a dual function with their involvement in olfaction and gustation. Results from mating experiments show that two HarmIRs (IR1.2 and IR75d) expression is significantly up-regulated in antennae of mated female moths. However, no expression difference is observed between unmated female and male adults, suggesting an association with female host-searching behaviors. Our current study has greatly extended the IR gene repertoire resource in Lepidoptera, and more importantly, identifies potential IR candidates for olfactory, gustatory and oviposition behaviors in the cotton bollworm.

Crystal structure of methyl (E)-4-[2-(8-hy-droxy-quinolin-2-yl)vin-yl]benzoate.

The title compound, C19H15NO3, was synthesized by a Perkin reaction of 2-methyl-8-hy-droxy-quinoline and 4-formyl-2-methyl-benzoate in acetic anhydride under a nitro-gen atmosphere. The mol-ecule has an E conformation about the C=C bond, and the quinoline ring system and the benzene ring are inclined to one another by 29.22 (7)°. There is an intra-molecular O-H⋯N hydrogen bond in the 8-hy-droxy-quinoline moiety. In the crystal, mol-ecules are linked by pairs of O-H⋯O hydrogen bonds, forming inversion dimers with an R22(28) ring motif. The dimers are linked by C-H⋯O hydrogen bonds and C-H⋯π inter-actions, forming sheets parallel to plane (10-1).