Insecticidal activity of Origanum majorana L. essential oil as anti‐cholinergic agent

The present study was focused on exploring the presence of active compounds in Origanum majorana essential oil (OmEO), and its various knock‐down effects against the rice moth, Corcyra cephalonica. GC–MS analysis detected the existence of major compounds such as monoterpenes, cis‐β‐terpineol and terpinen‐4‐ol with the total proportion of 52.16%. Fumigant toxicity against adult and larvae was calculated with an LC₅₀ value of 11.31 and 49.83 μL/L air, respectively. The contact toxicity against adult, pupa, larvae and eggs was observed with LC₅₀ value 2.54, 0.95, 2.78, and 0.49 μL/L, respectively. Furthermore, the influential repellent behavior against adults has been observed. Acetylesterase (AChE) inhibition activity of OmEO was observed against adult and larvae of C. cephalonica with an IC₅₀ value of 35.89 and 118.54 μL/mL, respectively. Moreover, computational docking study revealed the binding affinity of Cis‐β‐terpineol and terpinen‐4‐ol towards the active binding sites of AChE. On the other hand, Fluorescence‐assisted cytometry and comet assay confirmed the cytotoxic and genotoxic effect of OmEO at various concentrations on C. cephalonica. Altogether, the results showed the knock‐down effect of OmEO against C. cephalonica, and it could be a potential biocontrol measure against the stored product pest.     

福州市公园外来入侵植物初步调查与分析

[目的] 了解福州市公园的外来入侵植物种类组成,分析其原产地及入侵等级等情况,能够为福州外来入侵植物的扩散、防控以及生物多样性保护提供参考依据。[方法] 对福州市4个区49个公园的外来入侵植物种类、原产地、生活型、入侵频度、危害程度（入侵等级）等进行调查和分析。[结果] 在调查的福州市所有公园内均有入侵植物分布,目前有入侵植物66种,隶属25科,其中菊科、豆科、苋科3个科为优势科,共计33种（占50.00%）;从来源上看,大多数原产于美洲,其次是非洲、欧洲、亚洲;以草本植物为主,共有55种（占83.30%）;从入侵频度看,入侵频度超过50%的入侵植物有7种,其中小蓬草的频度最高,为87.76%;从入侵等级来看,其中恶性（1级）入侵植物16种,严重（2级）入侵植物14种,局部（3级）入侵植物12种,一般（4级）入侵植物11种,有待观察类（5级）13种。[结论] 当前福州市公园内的外来植物入侵现象比较严重,应当加强该区域的入侵植物监测与预警,防止入侵植物扩散从而造成重大生态危害。     

Molecular identification and functional analysis of Niemann-Pick type C2 protein in Macrocentrus cingulum Brischke (Hymenoptera: Braconidae)

Niemann-Pick type C2 (NPC2) proteins in arthropods have been extensively differentiated and possibly duplicated according to environmental conditions and are probable to have different functions. The participation of NPC2 proteins in chemical communication in arthropods brings new objectives in environmental-friendly strategies for pest population control. In this study, NPC2 gene in Macrocentrus cingulum (McinNPC2) was newly identified by rapid amplification cDNA ends (RACE) technology. McinNPC2 amino acid sequence alignment with other representative NPC2 annotates to evaluate the highly conserved consensus amino acids, but with odorant binding proteins in M. cingulum show that only one consensus amino acid. Primary six-cysteine structures that are same to odorant binding proteins in M. cingulum were observed in McinNPC2. Phylogenetic analysis of McinNPC2 indicated that the nearest monophyletic group forming one clade with high posterior probability values clusters as Cyphomyrmex costatus (CcosNPC2) whereas the nearest evolutionary relation group as some odorant binding proteins. Moreover, quantitative real-time PCR (qPCR) measurements show that the McinNPC2 gene expression level in various tissues of the female is significantly and ubiquitously higher than in male, whereas the highest expression level in female antennae. We further explore the binding characterization of recombinant McinNPC2 to candidate odor molecules and did the modeling and docking simulations. The results showed ligands binding specificity and docking tests results indicate that β-ionone, an aroma compound commonly found in essential oils, can strongly bind with McinNPC2. In conclusion, we proposed that McinNPC2 may be involved in chemical communication and play roles in perception of plant volatiles.     

Requirement of PEA3 for Transcriptional Activation of FAK Gene in Tumor Metastasis

Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase critically involved in cancer metastasis. We found an elevation of FAK expression in highly metastatic melanoma B16F10 cells compared with its less metastatic partner B16F1 cells. Down-regulation of the FAK expression by either small interfering RNA or dominant negative FAK (FAK Related Non-Kinase, FRNK) inhibited the B16F10 cell migration in vitro and invasiveness in vivo. The mechanism by which FAK activity is up-regulated in highly metastatic cells remains unclear. In this study, we reported for the first time that one of the Est family proteins, PEA3, is able to transactivate FAK expression through binding to the promoter region of FAK. We identified a PEA3-binding site between nucleotides −170 and +43 in the FAK promoter that was critical for the responsiveness to PEA3. A stronger affinity of PEA3 to this region contributed to the elevation of FAK expression in B16F10 cells. Both in vitro and in vivo knockdown of PEA3 gene successfully mimicked the cell migration and invasiveness as that induced by FAK down-regulation. The activation of the well-known upstream of PEA3, such as epidermal growth factor, JNK, and ERK can also induce FAK expression. Furthermore, in the metastatic human clinic tumor specimens from the patients with human primary oral squamous cell carcinoma, we observed a strong positive correlation among PEA3, FAK, and carcinoma metastasis. Taking together, we hypothesized that PEA3 might play an essential role in the activation of the FAK gene during tumor metastasis.     

Computational identification of novel biochemical systems involved in oxidation,glycosylation and other complex modifications of bases in DNA

Discovery of the TET/JBP family of dioxygenases that modify bases in DNA has sparked considerable interest in novel DNA base modifications and their biological roles. Using sensitive sequence and structure analyses combined with contextual information from comparative genomics, we computationally characterize over 12 novel biochemical systems for DNA modifications. We predict previously unidentified enzymes, such as the kinetoplastid J-base generating glycosyltransferase (and its homolog GREB1), the catalytic specificity of bacteriophage TET/JBP proteins and their role in complex DNA base modifications. We also predict the enzymes involved in synthesis of hypermodified bases such as alpha-glutamylthymine and alpha-putrescinylthymine that have remained enigmatic for several decades. Moreover, the current analysis suggests that bacteriophages and certain nucleo-cytoplasmic large DNA viruses contain an unexpectedly diverse range of DNA modification systems, in addition to those using previously characterized enzymes such as Dam, Dcm, TET/JBP, pyrimidine hydroxymethylases, Mom and glycosyltransferases. These include enzymes generating modified bases such as deazaguanines related to queuine and archaeosine, pyrimidines comparable with lysidine, those derived using modified S-adenosyl methionine derivatives and those using TET/JBP-generated hydroxymethyl pyrimidines as biosynthetic starting points. We present evidence that some of these modification systems are also widely dispersed across prokaryotes and certain eukaryotes such as basidiomycetes, chlorophyte and stramenopile alga, where they could serve as novel epigenetic marks for regulation or discrimination of self from non-self DNA. Our study extends the role of the PUA-like fold domains in recognition of modified nucleic acids and predicts versions of the ASCH and EVE domains to be novel ‘readers’ of modified bases in DNA. These results open opportunities for the investigation of the biology of these systems and their use in biotechnology.     

SPSSM8: An accurate approach for predicting eight-state secondary structures of proteins

Protein eight-state secondary structure prediction is challenging, but is necessary to determine protein structure and function. Here, we report the development of a novel approach, SPSSM8, to predict eight-state secondary structures of proteins accurately from sequences based on the structural position-specific scoring matrix (SPSSM). The SPSSM has been successfully utilized to predict three-state secondary structures. Now we employ an eight-state SPSSM as a feature that is obtained from sequence structure alignment against a large database of 9 million sequences with putative structural information. The SPSSM8 uses a low sequence identity dataset (9062 entries) as a training set and conditional random field for the classification algorithm. The SPSSM8 achieved an average eight-state secondary structure accuracy (Q8) of 71.7% (Q3, 81.6%) for an independent testing set (463 entries), which had an improved accuracy of 10.1% and 4.6% compared with SSPro8 and CNF, respectively, and significantly improved the accuracy of eight-state secondary structure prediction. For CASP 9 dataset (92 entries) the SPSSM8 achieved a Q8 accuracy of 80.1% (Q3, 83.0%). The SPSSM8 was confirmed as an outstanding predictor for eight-state secondary structures of proteins. SPSSM8 is freely available at http://cal.tongji.edu.cn/SPSSM8.     

Cloning of the Lentinula edodes B mating-type locus and identification of the genetic structure controlling B mating

During the life cycle of heterothallic tetrapolar Agaricomycetes such as Lentinula edodes (Berk.) Pegler, the mating type system, composed of unlinked A and B loci, plays a vital role in controlling sexual development and resulting formation of the fruit body. L. edodes is produced worldwide for consumption and medicinal purposes, and understanding its sexual development is therefore of great importance. A considerable amount of mating type factors has been indicated over the past decades but few genes have actually been identified, and no complete genetic structures of L. edodes B mating-type loci are available. In this study, we cloned the matB regions from two mating compatible L. edodes strains, 939P26 and 939P42. Four pheromone receptors were identified on each new matB region, together with three and four pheromone precursor genes in the respective strains. Gene polymorphism, phylogenetic analysis and distribution of pheromone receptors and pheromone precursors clearly indicate a bipartite matB locus, each sublocus containing a pheromone receptor and one or two pheromone precursors. Detailed sequence comparisons of genetic structures between the matB regions of strains 939P42, 939P26 and a previously reported strain SUP2 further supported this model and allowed identification of the B mating type subloci borders. Mating studies confirmed the control of B mating by the identified pheromone receptors and pheromones in L. edodes.     

An ITS-based phylogenetic framework for the genus Vorticella: finding the molecular and morphological gaps in a taxonomically difficult group

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers—fast-evolving internal transcribed spacer (ITS) regions—in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella. Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta, indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.     

Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast

The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast.