D 4h H©K4H4-: a planar tetracoordinate hydrogen global minimum.

Herein we report a square-like D4h H©K4H4- anion with one planar tetracoordinate hydrogen (ptH) center, which is the global minimum (GM) structure and possesses good dynamic stability. The planar structure of the system is preserved by four peripheral K-H-K three-center two-electron (3c-2e) σ bonds together with one 5c-2e σ bond over the HK4 core. The multicenter ionic bonds dominate the stability of ptH, while the contribution of qualitative σ aromaticity is extremely limited.

XB2Bi2 (X = Si, Ge, Sn, Pb): Penta-Atomic Planar Tetracoordinate Si/Ge/Sn/Pb Clusters with 20 Valence Electrons.

Planar tetracoordinate silicon, germanium, tin, and lead (ptSi/Ge/Sn/Pb) species are scarce and exotic. Here, we report a series of penta-atomic ptSi/Ge/Sn/Pb XB2Bi2 (X = Si, Ge, Sn, Pb) clusters with 20 valence electrons (VEs). Ternary XB2Bi2 (X = Si, Ge, Sn, Pb) clusters possess beautiful fan-shaped structures, with a Bi-B-B-Bi chain surrounding the central X core. The unbiased density functional theory (DFT) searches and high-level CCSD(T) calculations reveal that these ptSi/Ge/Sn/Pb species are the global minima on their potential energy surfaces. Born-Oppenheimer molecular dynamics (BOMD) simulations indicate that XB2Bi2 (X = Si, Ge, Sn, Pb) clusters are robust. Bonding analyses indicate that 20 VEs are perfect for the ptX XB2Bi2 (X = Si, Ge, Sn, Pb): two lone pairs of Bi atoms; one 5c-2e π, and three σ bonds (two Bi-X 2c-2e and one B-X-B 3c-2e bonds) between the ligands and X atom; three 2c-2e σ bonds and one delocalized 4c-2e π bond between the ligands. The ptSi/Ge/Sn/Pb XB2Bi2 (X = Si, Ge, Sn, Pb) clusters possess 2π/2σ double aromaticity, according to the (4n + 2) Hückel rule.

Proteome exploration to provide a resource for the investigation of Ganoderma lucidum.

Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with "binding", "catalytic activity", and "hydrolase activity" having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

Lectin from Agrocybe aegerita as a glycophenotype probe for evaluation of progression and survival in colorectal cancer.

BACKGROUND: Agrocybe aegerita Lectin (AAL) has been identified to have high affinity for sulfated and α2-3- linked sialic acid glycoconjugates, especially the sulfated and sialyl TF (Thomsen-Friedenreich) disaccharide. This study was conducted to investigate the clinicopathological and prognostic value of AAL in identifying aberrant glycosylation in colorectal cancer (CRC). MATERIALS AND METHODS: Glycoconjugate expression in 59 CRC tissues were detected using AAL-histochemistry. Clinicopathological associates of expression were analyzed with chi- square test or Fisher's exact test. Relationships between expression and the various clinicopathological parameters was estimated using Kaplan-Meier analysis and Cox regression models. RESULTS: AAL specific glycoconjugate expression was significantly higher in tumor than corresponding normal tissues (66.1% and 46.1%, respectively, p=0.037), correlating with depth of invasion (p=0.015) and TNM stage (p=0.024). Patients with lower expression levels had a significantly higher survival rate than those with higher expression (p=0.046 by log rank test and p=0.047 by Breslow test for overall survival; p=0.054 by log rank test and P=0.038 by Breslow test for progress free survival). A marginally significant association was found between AAL specific glycoconjugate expression and overall survival by univariate Cox regression analysis (p=0.059). CONCLUSIONS: Lower AAL specific glycoconjugate expression is a significant favorable prognostic factor for overall and progress free survival in CRC. This is the first report about the employment of AAL for histochemical analysis of cancer tissues. The binding characteristics of AAL means it has potential to become a powerful tool for the glycan investigation and clinical application.

Deep insight into the Ganoderma lucidum by comprehensive analysis of its transcriptome.

BACKGROUND: Ganoderma lucidum is a basidiomycete white rot fungus and is of medicinal importance in China, Japan and other countries in the Asiatic region. To date, much research has been performed in identifying the medicinal ingredients in Ganoderma lucidum. Despite its important therapeutic effects in disease, little is known about Ganoderma lucidum at the genomic level. In order to gain a molecular understanding of this fungus, we utilized Illumina high-throughput technology to sequence and analyze the transcriptome of Ganoderma lucidum. METHODOLOGY/PRINCIPAL FINDINGS: We obtained 6,439,690 and 6,416,670 high-quality reads from the mycelium and fruiting body of Ganoderma lucidum, and these were assembled to form 18,892 and 27,408 unigenes, respectively. A similarity search was performed against the NCBI non-redundant nucleotide database and a customized database composed of five fungal genomes. 11,098 and 8, 775 unigenes were matched to the NCBI non-redundant nucleotide database and our customized database, respectively. All unigenes were subjected to annotation by Gene Ontology, Eukaryotic Orthologous Group terms and Kyoto Encyclopedia of Genes and Genomes. Differentially expressed genes from the Ganoderma lucidum mycelium and fruiting body stage were analyzed, resulting in the identification of 13 unigenes which are involved in the terpenoid backbone biosynthesis pathway. Quantitative real-time PCR was used to confirm the expression levels of these unigenes. Ganoderma lucidum was also studied for wood degrading activity and a total of 22 putative FOLymes (fungal oxidative lignin enzymes) and 120 CAZymes (carbohydrate-active enzymes) were predicted from our Ganoderma lucidum transcriptome. CONCLUSIONS: Our study provides comprehensive gene expression information on Ganoderma lucidum at the transcriptional level, which will form the foundation for functional genomics studies in this fungus. The use of Illumina sequencing technology has made de novo transcriptome assembly and gene expression analysis possible in species that lack full genome information.