bluuebunny/crossref_metadata_2025 huggingface dataset:
Ab initioStudy of Mechanism of Forming Germanic Bis-Heterocyclic Compound Between Dichloro-Germylene Carbene (Cl2Ge = C:) and Formaldehyde
Authors: Lu Xiu-hui , Che Xin , Lian Zhen-xia , Li Yong-qing
Published: September 2010

The mechanism of the cycloaddition reaction of forming germanic bis-heterocyclic compound between singlet dichloro-germylene carbene and formaldehyde has been investigated with CCSD(T)//MP2/6–31G* method, from the potential energy profile, we predict that the reaction has two competitive dominant reaction pathways. The presented rule of this reaction: the 2p unoccupied orbital of the C atom in dichloro-germylene carbene insert the π orbital of formaldehyde from oxygen side, resulting in the formation of intermediate. In the intermediate and between two reactants, because of the two bonding π orbital in dichloro-germylene carbene and formaldehyde have occurred [2+2] cycloaddition reaction, forming two four-membered ring compounds in which Ge and O are in the opposite orientation and in the syn-position, respectively. Because of the unsaturated property of C atom from carbene in the two four-membered ring compounds, they further reacts with formaldehyde, resulting in the generation of two germanic bis-heterocyclic compounds.
Density Functional Study of AunCo (n= 1–7)
Authors: Yang Ji-xian , Guo Jian-jun , Die Dong
Published: September 2010

Cobalt-doped gold clusters AunCo (n = 1–7) are systematically investigated for the possible stable geometrical configurations and relative stabilities of the lowest-lying isomers using density-functional theory at B3LYP/LanL2DZ level. Several low-lying isomers were determined, and many of them are in electronic configurations with a high spin multiplicity. The results indicate that the ground-state AunCo (n = 1–7) clusters adopt a planar structure except for n = 7. The stability trend of the AunCo (n = 1–7) clusters shows that the Au2Co clusters are magic cluster with high stability.
First-principle Study of AunSc (n= 2–13) Clusters
Authors: Ge Gui-xian , Yan Hong-xia , Jing Qun
Published: September 2010

The geometries, stabilities, electronic, and magnetic properties of AunSc clusters have been systematically investigated by density functional theory. The lowest energy structures of AunSc favor planar structure and the doped Sc atom does not disturb the frame of Aun clusters with n ≤ 11. For n ≥ 12, Sc atom is fully encapsulated by the Au cages. From the analysis of the second-order energy difference, the fragmentation energies, vertical ionization potential, vertical electron affinity, and HOMO-LUMO gap, the clusters with odd Au atoms possess relatively higher stabilities than their neighbor size. The doping of Sc atom can greatly improve the stability and change the sequence of chemical activity for Aun. For n ≤ 11, the total magnetic moments of AunSc appear the alternation between 0.00 and 1.00 μB. The total magnetic moments are quenched when Sc is trapped into the Au cages with n ≥ 12.
Symmetric Ferroelectric Switching in Ferroelectric Vinylidene Fluoride and Trifluoroethylene Copolymer Films
Authors: Zhu Guo-dong , Luo Xiao-ya , Zhang Ji-hao , Yan Xue-jian
Published: September 2010

We report the observation of asymmetric switching dual peaks in ferroelectric copolymer films. These dual peaks occurs when the poling electric field is just below the coercive field and can be removed by continuous application of high enough switching voltage. Our experimental observations can be explained by the injection and the redistribution of space charges in ferroelectric films.
Synthesis and Characterization of Novel N-doped TiO2 Photocatalyst with Visible Light Active
Authors: Peng Feng , Liu Yi , Wang Hong-juan , Yu Hao , Yang Jian
Published: September 2010

A novel N-doped TiO2 (N1-N2-TiO2) with substitutional and interstitial N impurities simultaneously was successfully synthesized. The catalyst was characterized by X-ray diffraction, X-ray photoelectron spectroscopy, diffuse reflectance spectroscopy, photoluminescence, and electron paramagnetic resonance. The results demonstrated that the nitrogen was substituted for the lattice oxygen atoms, and was also interstitially doped into the TiO2 lattice. The photocatalytic tests indicated that the N1-N2-TiO2 showed the highest photocatalytic activities of all the N-doped TiO2 under visible light, attributing to the synergetic effect of substitutional and interstitial nitrogen of N-doped TiO2.
Oxidation of Carbon Supports at Fuel Cell Cathodes: Differential Electrochemical Mass Spectrometric Study
Authors: Li Ming-fang , Tao Qian , Liao Ling-wen , Xu Jie , Cai Jun , Chen Yan-xia
Published: September 2010

The effects of O2 and the supported Pt nano-particles on the mechanisms and kinetics of the carbon support corrosion are investigated by monitoring the CO2 production using differential electrochemical mass spectrometry in a dual-thin layer flow cell. Carbon can be oxidized in different distinct potential regimes; O2 accelerates carbon oxidation, the rates of CO2 production from carbon oxidation in O2 saturated solution are two times of that in N2 saturated solution at the same potential; Pt can catalyze the carbon oxidation, with supported Pt nanoparticles, the overpotential for carbon oxidation is much smaller than that without loading in the carbon electrode. The mechanism for the enhanced carbon oxidation by Pt and O2 are discussed.
Effect of Cadmium Substitution on Structural and Magnetic Properties of Nano Sized Nickel Ferrite
Authors: Pralhadrao Jadhav Sanjay , Ghanshamji Toksha Bhagwan , Marutirao Jadhav Kamalakar , Dadarao Shinde Narayan
Published: September 2010

The structure and crystal phase of the nanocrystalline powders of Ni1–xCdxFe2O4 (0≤x≤0.5) mixed ferrite, synthesized by wet chemical co-precipitation method, were characterized by X-ray diffraction. Results showed that the lattice parameter increased with increasing Cd concentration. Microstructure was studied by scanning electron microscopy. TG/DTA studies were carried out on co-precipitated sulphate complexes. These studies revealed the low ferritization temperature (650 °C) of the ferrite system synthesized by presently adopted route of synthesis and occurrence of simultaneous decomposition and ferritization processes. Further studies by infrared spectroscopy were also conducted. Moreover, magnetic properties of the prepared nanoparticles were studied by magnetization and a.c. susceptibility measurements. The response of prepared Ni1–xCdxFe2O4 mixed ferrites to magnetic field was investigated. Results show that, magnetic susceptibility, Curie temperature, and effective magnetic moment decreased as the Cd content increases.
Room Temperature Magnetic Behavior of Sol-Gel Synthesized Mn Doped ZnO
Authors: Saleem Murtaza , A. Siddiqi Saadat , Atiq Shahid , Sabieh Anwar M. , Riaz Saira
Published: September 2010

Mn doped ZnO nano-crystallites were synthesized by state of the art sol-gel derived auto-combustion technique. As-burnt powder was investigated with different characterization techniques to explore the properties of Mn doped ZnO dilute magnetic semiconductor. X-ray diffraction measurements indicate that Mn doped ZnO retain wurtzite type hexagonal crystal structure like ZnO. Compositional and morphological studies were carried out by energy dispersive X-ray analysis and scanning electron microscopy, respectively. Temperature dependent resistivity of the sample exhibited the semiconducting behavior of the DMS material. Room temperature magnetic properties determined by vibrating sample magnetometer, revealed the presence of ferromagnetic and diamagnetic contributions in Mn doped ZnO.
Facile H2O2 Hydrothermal Synthesis of Bimodal Mesoporous Silica MCM-48 Spheres
Authors: Tian Dong , Yong Guo-ping , Tong Hong-wu , Liu Shao-min
Published: September 2010

The ordered bimodal mesoporous silica MCM-48 spheres were facile synthesized by mild-temperature post-synthesis H2O2 hydrothermal treatment of as-synthesized MCM-48. The results showed that H2O2 is indispensable for simultaneously removing organic templates and forming ordered bimodal mesoporous silica MCM-48 spheres. The bimodal mesoporous MCM-48 was characterized by X-ray diffraction, transmission electron micrographs, FT-IR, and N2 adsorption-desorption, and a possible mechanism was proposed for the formation of bimodal mesoporous MCM-48.
Rheological Behavior of Aqueous Solutions of Cationic Guar in Presence of Oppositely Charged Surfactant
Authors: Li Hua-zhen , Yang Hai-yang , Xie Yong-jun , Li Hua-yu , He Ping-sheng
Published: September 2010

The cationic guar (CG) is synthesized and the rheological behavior of aqueous solutions of CG in the presence of sodium dodecyl sulfate (SDS) is studied in detail. The steady viscosity measurements show that the zero shear viscosity enhancement can be almost 3 orders of magnitude as the concentration of SDS increases from 0 to 0.043%. The gel-like formation is observed as the concentration of SDS is greater than 0.016%. The oscillatory rheological measurements of CG solutions in the presence of SDS show that the crossover modulus is almost independent of the concentration of SDS whereas the apparent relaxation time increases swiftly upon increasing the concentration of SDS. The experimental results indicate that the strength rather than the number of the cross-links is greatly affected by SDS molecules. The mechanism concerning the effect of SDS upon the rheology of CG solutions can be coined by the two-stage model. Before the formation of cross-links at the critical concentration, the electrostatic interaction between SDS and cationic site of CG chains plays a key role and the SDS molecules bind to CG chains through the electrostatic interaction. After the formation of cross-links at the concentration greater than the critical concentration, the cooperative hydrophobic interaction become dominant and SDS molecules bind to the cross-links through the hydrophobic interaction. The rheological behavior of aqueous solutions of CG in the presence of SDS is chiefly determined by the micelle-like cross-links between CG chains. In fact, the flow activation energy of CG solution, obtained from the temperature dependence of the apparent relaxation time, falls in the range of transferring a hydrophobic tail of SDS from the micelle to an aqueous environment.
The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports
Authors: Wohlgemuth Gert , Haldiya Pradeep Kumar , Willighagen Egon , Kind Tobias , Fiehn Oliver
Published: September 2010

Summary: Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies. The best way to annotate metabolites is by chemical structures, encoded by the International Chemical Identifier code (InChI) or InChIKey. We have implemented a web-based Chemical Translation Service that performs batch conversions of the most common compound identifiers, including CAS, CHEBI, compound formulas, Human Metabolome Database HMDB, InChI, InChIKey, IUPAC name, KEGG, LipidMaps, PubChem CID+SID, SMILES and chemical synonym names. Batch conversion downloads of 1410 CIDs are performed in 2.5 min. Structures are automatically displayed.

Implementation: The software was implemented in Groovy and JAVA, the web frontend was implemented in GRAILS and the database used was PostgreSQL.

Availability: The source code and an online web interface are freely available. Chemical Translation Service (CTS): http://cts.fiehnlab.ucdavis.edu

Contact:  ofiehn@ucdavis.edu
Robust and accurate data enrichment statistics via distribution function of sum of weights
Authors: Stojmirović Aleksandar , Yu Yi-Kuo
Published: September 2010

Motivation: Term-enrichment analysis facilitates biological interpretation by assigning to experimentally/computationally obtained data annotation associated with terms from controlled vocabularies. This process usually involves obtaining statistical significance for each vocabulary term and using the most significant terms to describe a given set of biological entities, often associated with weights. Many existing enrichment methods require selections of (arbitrary number of) the most significant entities and/or do not account for weights of entities. Others either mandate extensive simulations to obtain statistics or assume normal weight distribution. In addition, most methods have difficulty assigning correct statistical significance to terms with few entities.

Results: Implementing the well-known Lugananni–Rice formula, we have developed a novel approach, called SaddleSum, that is free from all the aforementioned constraints and evaluated it against several existing methods. With entity weights properly taken into account, SaddleSum is internally consistent and stable with respect to the choice of number of most significant entities selected. Making few assumptions on the input data, the proposed method is universal and can thus be applied to areas beyond analysis of microarrays. Employing asymptotic approximation, SaddleSum provides a term-size-dependent score distribution function that gives rise to accurate statistical significance even for terms with few entities. As a consequence, SaddleSum enables researchers to place confidence in its significance assignments to small terms that are often biologically most specific.

Availability: Our implementation, which uses Bonferroni correction to account for multiple hypotheses testing, is available at http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/mn/enrich/. Source code for the standalone version can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/SaddleSum/.

Contact:  yyu@ncbi.nlm.nih.gov

Supplementary information: Supplementary materials are available at Bioinformatics online.
SBML2TikZ: supporting the SBML render extension in LaTeX
Authors: Shen Si Yuan , Bergmann Frank , Sauro Herbert M.
Published: September 2010

Motivation: The SBML Render Extension enables coloring and shape information of biochemical models to be stored in the Systems Biology Markup Language (SBML). Rendering of this stored graphical information in a portable and well supported system such as TeX would be useful for researchers preparing documentation and presentations. In addition, since the Render Extension is not yet supported by many applications, it is helpful for such rendering functionality be extended to the more popular CellDesigner annotation as well.

Results: SBML2TikZ supports automatic generation of graphics for biochemical models in the popular TeX typesetting system. The library generates a script of TeX macro commands for the vector graphics languages PGF/TikZ that can be compiled into scalable vector graphics described in a model.

Availability: Source code, documentation and compiled binaries for the SBML2TikZ library can be found at http://www.sbml2tikz.org. In addition, a web application is available at http://www.sys-bio.org/layout

Contact:  hsauro@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ODES: an overlapping dense sub-graph algorithm
Authors: Long James , Hartman Chris
Published: September 2010

Summary: Enumeration of the dense sub-graphs of a graph is of interest in community discovery and membership problems, including dense sub-graphs that overlap each other. Described herein is ODES (Overlapping DEnse Sub-graphs), pthreads parallelized software to extract all overlapping maximal sub-graphs whose densities are greater than or equal to a specified cutoff density of at least 1/2.

Availability and Implementation:  http://dense.sf.net

Contact:  jlong@alaska.edu
Fixed point characterization of biological networks with complex graph topology
Authors: Radde N.
Published: September 2010

Motivation: Feedback circuits are important motifs in biological networks and part of virtually all regulation processes that are needed for a reliable functioning of the cell. Mathematically, feedback is connected to complex behavior of the systems, which is often related to bifurcations of fixed points. Therefore, several approaches for the investigation of fixed points in biological networks have been developed in recent years. Many of them assume the fixed point coordinates to be known, and an efficient way to calculate the entire set of fixed points for interrelated feedback structures is highly desirable.

Results: In this article, we consider regulatory network models, which are differential equations with an underlying directed graph that illustrates independencies among variables. We introduce the circuit-breaking algorithm (CBA), a method that constructs one-dimensional characteristics for these network models, which inherit important information about the system. In particular, fixed points are related to the zeros of these characteristics. The CBA operates on the graph topology, and results from graph theory are used in order to make calculations efficient. Our framework provides a general scheme for analyzing network models in terms of interrelated feedback circuits. The efficiency of the approach is demonstrated on a model for calcium oscillations based on experiments in hepatocytes, which consists of several interrelated feedback circuits.

Contact:  radde@ist.uni-stuttgart.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Novel method for similarity analysis and protein sub-cellular localization prediction
Authors: Liao Bo , Liao Benyou , Sun Xingming , Zeng Qingguang
Published: September 2010

Motivation: Biological sequence was regarded as an important study by many biologists, because the sequence contains a large number of biological information, what is helpful for scientists' studies on biological cells, DNA and proteins. Currently, many researchers used the method based on protein sequences in function classification, sub-cellular location, structure and functional site prediction, including some machine-learning methods. The purpose of this article, is to find a new way of sequence analysis, but more simple and effective.

Results: According to the nature of 64 genetic codes, we propose a simple and intuitive 2D graphical expression of protein sequences. And based on this expression we give a new Euclidean-distance method to compute the distance of different sequences for the analysis of sequence similarity. This approach contains more sequence information. A typical phylogenetic tree constructed based on this method proved the effectiveness of our approach. Finally, we use this sequence-similarity-analysis method to predict protein sub-cellular localization, in the two datasets commonly used. The results show that the method is reasonable.

Contact:  dragonbw@163.com
Will depleted populations of Pacific salmon recover under persistent reductions in survival and catastrophic mortality events?
Authors: Holt Carrie A.
Published: September 2010

Holt, C. A. 2010. Will depleted populations of Pacific salmon recover under persistent reductions in survival and catastrophic mortality events? – ICES Journal of Marine Science, 67: 2018–2026. Under Canada's Wild Salmon Policy, benchmarks between zones of biological status are required to distinguish populations requiring conservation attention (Red and Amber zones) from those that can be managed for production (Green zone). The recovery of depleted populations (i.e. from Red to Green) will depend in part on the choice of the lower benchmark. At a minimum, that benchmark should be set high enough to allow recovery within an acceptable time-frame in the absence of targeted fishing. Currently, benchmarks are evaluated and selected using simulation models that assess the probability of recovery to spawner abundance associated with the maximum sustainable yield within a specified time-frame. Guided by case examples, the evaluation is extended to include two scenarios of future conditions: persistent reductions in survival rates below the replacement level; and increased frequency of catastrophic mortality (die-off) events. Probabilities of recovery appear to be more sensitive to persistent reductions in survival than to increased probability of die-off events. The current lower benchmarks on spawner abundance and fishing mortality might not be sufficiently precautionary to allow recovery under those conditions.
Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components
Authors: Mahévas Stéphanie , Trenkel Verena M. , Doray Mathieu , Peyronnet Arnaud
Published: September 2010

Mahévas, S., Trenkel, V. M., Doray, M., and Peyronnet, A. 2011. Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components. – ICES Journal of Marine Science, 68: 107–118. Several factors affect trawl catchability: (i) gear and vessel technical characteristics, (ii) anthropogenic factors, and (iii) biological factors. The objectives of this study were to assess the relative contribution of each factor to variations in hake (Merluccius merluccius) landings by the French trawler fleet operating on the shelf of the northern Bay of Biscay (ICES Subdivision VIIIa). Using generalized linear models, the impact of technical and anthropogenic factors was evaluated using landings per unit effort (lpue) obtained from logbooks. Variations in hake lpue were explained primarily by anthropogenic factors. For studying the biological components of catchability, the results of a scientific trawl survey in July 2006 involving three similar trawlers of the French trawler fleet were used. Daytime accessibility to large hake was lower than at night, and about zero for small hake (<19 cm). Estimates of spatial variation made using generalized linear mixed models showed a patchy fine-scale spatial distribution, but a random larger-scale distribution of hake over the area surveyed.
Regulation of Motility in Erwinia carotovora subsp. carotovora: Quorum-Sensing Signal Controls FlhDC, the Global Regulator of Flagellar and Exoprotein Genes, by Modulating the Production of RsmA, an RNA-Binding Protein
Authors: Chatterjee Asita , Cui Yaya , Chakrabarty Pranjib , Chatterjee Arun K.
Published: September 2010

Erwinia carotovora subsp. carotovora causes soft-rotting (tissue-macerating) disease in many plants and plant organs. Although pectinases are the primary determinants of virulence, several ancillary factors that augment bacterial virulence have also been identified. One such factor is bacterial motility. Flagellum formation and bacterial movement are regulated in many enterobacteria, including E. carotovora subsp. carotovora, by FlhDC, the master regulator of flagellar genes and FliA, a flagellum-specific σ factor. We document here that motility of E. carotovora subsp. carotovora is positively regulated by the quorum-sensing signal, N-acylhomoserine lactone (AHL), and negatively regulated by RsmA, a post-transcriptional regulator. RsmA, an RNA-binding protein, causes translational repression and promotes RNA decay. Our data show that RsmA negatively regulates flhDC and fliA expression. Moreover, the chemical stabilities of transcripts of these genes are greater in an RsmA– mutant than in RsmA+ bacteria. These observations contrast with positive regulation of flhDC and motility by CsrA (= RsmA) in Escherichia coli. In the absence of AHL, the AHL receptors ExpR1/ExpR2 (= AhlR) in Erwinia carotovora subsp. carotovora negatively regulate motility and expression of flhDC and fliA by activating RsmA production. In the presence of AHL, regulatory effects of ExpR1/ExpR2 are neutralized, resulting in reduced levels of rsmA expression and enhanced motility.
The Arabidopsis Downy Mildew Resistance Gene RPP8 Is Induced by Pathogens and Salicylic Acid and Is Regulated by W Box cis Elements
Authors: Mohr Toni J. , Mammarella Nicole D. , Hoff Troy , Woffenden Bonnie J. , Jelesko John G. , McDowell John M.
Published: September 2010

Plants disease resistance (R) genes encode specialized receptors that are quantitative, rate-limiting defense regulators. R genes must be expressed at optimum levels to function properly. If expression is too low, downstream defense responses are not activated efficiently. Conversely, overexpression of R genes can trigger autoactivation of defenses with deleterious consequences for the plant. Little is known about R gene regulation, particularly under defense-inducing conditions. We examined regulation of the Arabidopsis thaliana gene RPP8 (resistance to Hyaloperonospora arabidopsidis, isolate Emco5). RPP8 was induced in response to challenge with H. arabidopsidis or application of salicylic acid, as shown with RPP8-Luciferase transgenic plants and quantitative reverse-transcription polymerase chain reaction of endogenous alleles. The RPP1 and RPP4 genes were also induced by H. arabidopsidis and salicylic acid, suggesting that some RPP genes are subject to feedback amplification. The RPP8 promoter contains three W box cis elements. Site-directed mutagenesis of all three W boxes greatly diminished RPP8 basal expression, inducibility, and resistance in transgenic plants. Motif searches indicated that the W box is the only known cis element that is statistically overrepresented in Arabidopsis nucleotide-binding leucine-rich repeat promoters. These results indicate that WRKY transcription factors can regulate expression of surveillance genes at the top of the defense-signaling cascade.
Characterization of MoLDB1 Required for Vegetative Growth, Infection-Related Morphogenesis, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae
Authors: Li Ya , Liang Shen , Yan Xia , Wang Hong , Li Debao , Soanes Darren M. , Talbot Nicholas J. , Wang Zonghua , Wang Zhengyi
Published: September 2010

An insertional mutagenesis screen in the rice blast fungus, Magnaporthe oryzae, identified a novel mutant, A2-12-3, which is defective in infection-related morphogenesis and pathogenicity. Analysis of the mutation confirmed an insertion into MoLDB1, which putatively encodes an 806-amino-acid protein with a predicted LIM binding domain. Targeted gene deletion mutants of MoLDB1 were unable to produce asexual or sexual spores and were significantly impaired in vegetative growth and fungal virulence. The Δmoldb1 mutants also showed reduced expression of genes coding hydrophobic proteins (e.g. MPG1 and MHP1), resulting in an easily wettable phenotype in vegetative culture. Moreover, the expression of four genes encoding LIM proteins predicted from the M. oryzae genome was significantly downregulated by deletion of MoLDB1. Analysis of an M. oryzae strain expressing a MoLbd1-green fluorescent protein gene fusion was consistent with the protein being nuclear localized. When considered together, MoLdb1 appears to be involved in regulation of cell wall proteins, including hydrophobins and LIM proteins, and is essential for conidiation, sexual development, appressorium formation, and pathogenicity in M. oryzae.
Role of Cyclic di-GMP in Xylella fastidiosa Biofilm Formation, Plant Virulence, and Insect Transmission
Authors: Chatterjee Subhadeep , Killiny Nabil , Almeida Rodrigo P. P. , Lindow Steven E.
Published: September 2010

Xylella fastidiosa must coordinately regulate a variety of traits contributing to biofilm formation, host plant and vector colonization, and transmission between plants. Traits such as production of extracellular polysaccharides (EPS), adhesins, extracellular enzymes, and pili are expressed in a cell-density-dependent fashion mediated by a cell-to-cell signaling system involving a fatty acid diffusible signaling factor (DSF). The expression of gene PD0279 (which has a GGDEF domain) is downregulated in the presence of DSF and may be involved in intracellular signaling by modulating the levels of cyclic di-GMP. PD0279, designated cyclic di-GMP synthase A (cgsA), is required for biofilm formation, plant virulence, and vector transmission. cgsA mutants exhibited a hyperadhesive phenotype in vitro and overexpressed gumJ, hxfA, hxfB, xadA, and fimA, which promote attachment of cells to surfaces and, hence, biofilm formation. The mutants were greatly reduced in virulence to grape albeit still transmissible by insect vectors, although at a reduced level compared with transmission rates of the wild-type strain, despite the fact that similar numbers of cells of the cgsA mutant were acquired by the insects from infected plants. High levels of EPS were measured in cgsA mutants compared with wild-type strains, and scanning electron microscopy analysis also revealed a thicker amorphous layer surrounding the mutants. Overexpression of cgsA in a cgsA-complemented mutant conferred the opposite phenotypes in vitro. These results suggest that decreases of cyclic di-GMP result from the accumulation of DSF as cell density increases, leading to a phenotypic transition from a planktonic state capable of colonizing host plants to an adhesive state that is insect transmissible.
Regulatory Mechanisms of Exoribonuclease PNPase and Regulatory Small RNA on T3SS of Dickeya dadantii
Authors: Zeng Quan , Ibekwe A. Mark , Biddle Eulandria , Yang Ching-Hong
Published: September 2010

The type III secretion system (T3SS) is an essential virulence factor for many bacterial pathogens. Polynucleotide phosphorylase (PNPase) is one of the major exoribonucleases in bacteria and plays important roles in mRNA degradation, tRNA processing, and small RNA (sRNA) turnover. In this study, we showed that PNPase downregulates the transcription of T3SS structural and effector genes of the phytopathogenic bacterium Dickeya dadantii. This negative regulation of T3SS by PNPase occurs by repressing the expression of hrpL, encoding a master regulator of T3SS in D. dadantii. By reducing rpoN mRNA stability, PNPase downregulates the transcription of hrpL, which leads to a reduction in T3SS gene expression. Moreover, we have found that PNPase downregulates T3SS by decreasing hrpL mRNA stability. RsmB, a regulatory sRNA, enhances hrpL mRNA stability in D. dadantii. Our results suggest that PNPase decreases the amount of functional RsmB transcripts that could result in reduction of hrpL mRNA stability. In addition, bistable gene expression (differential expression of a single gene that creates two distinct subpopulations) of hrpA, hrpN, and dspE was observed in D. dadantii under in vitro conditions. Although PNPase regulates the proportion of cells in the high state and the low state of T3SS gene expression, it appears that PNPase is not the key switch that triggers the bistable expression patterns of T3SS genes.
Varied Movement Strategies Employed by Triple Gene Block–Encoding Viruses
Authors: Verchot-Lubicz Jeanmarie , Torrance Lesley , Solovyev Andrey G. , Morozov Sergey Yu , Jackson Andrew O. , Gilmer David
Published: September 2010

Several RNA virus genera belonging to the Virgaviridae and Flexiviridae families encode proteins organized in a triple gene block (TGB) that facilitate cell-to-cell and long-distance movement. The TGB proteins have been traditionally classified as hordei-like or potex-like based on phylogenetic comparisons and differences in movement mechanisms of the Hordeivirus and Potexvirus spp. However, accumulating data from other model viruses suggests that a revised framework is needed to accommodate the profound differences in protein interactions occurring during infection and ancillary capsid protein requirements for movement. The goal of this article is to highlight common features of the TGB proteins and salient differences in movement properties exhibited by individual viruses encoding these proteins. We discuss common and divergent aspects of the TGB transport machinery, describe putative nucleoprotein movement complexes, highlight recent data on TGB protein interactions and topological properties, and review membrane associations occurring during subcellular targeting and cell-to-cell movement. We conclude that the existing models cannot be used to explain all TGB viruses, and we propose provisional Potexvirus, Hordeivirus, and Pomovirus models. We also suggest areas that might profit from future research on viruses harboring this intriguing arrangement of movement proteins.
Pseudomonas syringae Virulence Factor Syringolin A Counteracts Stomatal Immunity by Proteasome Inhibition
Authors: Schellenberg Barbara , Ramel Christina , Dudler Robert
Published: September 2010

The peptide derivative syringolin A, a product of a mixed nonribosomal peptide and polyketide synthetase, is secreted by certain strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae. Syringolin A was shown to be a virulence factor for P. syringae pv. syringae B728a because disease symptoms on its host Phaseolus vulgaris (bean) were greatly reduced upon inoculation with syringolin A-negative mutants. Syringolin A's mode of action was recently shown to be irreversible proteasome inhibition. Here, we report that syringolin A-producing bacteria are able to open stomata and, thus, counteract stomatal innate immunity in bean and Arabidopsis. Syringolin A-negative mutants, which induce stomatal closure, can be complemented by exogenous addition of not only syringolin A but also MG132, a well-characterized and structurally unrelated proteasome inhibitor. This demonstrates that proteasome activity is crucial for guard cell function. In Arabidopsis, stomatal immunity was salicylic acid (SA)-dependent and required NPR1, a key regulator of the SA-dependent defense pathway whose proteasome-dependent turnover has been reported to be essential for its function. Thus, elimination of NPR1 turnover through proteasome inhibition by syringolin A is an attractive hypothesis to explain the observed inhibition of stomatal immunity by syringolin A.
Laser Capture Microdissection of Uredinia Formed by Melampsora larici-populina Revealed a Transcriptional Switch Between Biotrophy and Sporulation
Authors: Hacquard Stéphane , Delaruelle Christine , Legué Valérie , Tisserant Emilie , Kohler Annegret , Frey Pascal , Martin Francis , Duplessis Sébastien
Published: September 2010

The foliar rust caused by the basidiomycete Melampsora larici-populina is the main disease affecting poplar plantations in Europe. The biotrophic status of rust fungi is a major limitation to study gene expression of cell or tissue types during host infection. At the uredinial stage, infected poplar leaves contain distinct rust tissues such as haustoria, infection hyphae, and uredinia with sporogenous hyphae and newly formed asexual urediniospores. Laser capture microdissection (LCM) was used to isolate three areas corresponding to uredinia and subjacent zones in the host mesophyll for expression analysis with M. larici-populina whole-genome exon oligoarrays. Optimization of tissue preparation prior to LCM allowed isolation of RNA of good integrity for genome-wide expression profiling. Our results indicate that the poplar rust uredinial stage is marked by distinct genetic programs related to biotrophy in the host palisade mesophyll and to sporulation in the uredinium. A strong induction of transcripts encoding small secreted proteins, likely containing rust effectors, is observed in the mesophyll, suggesting a late maintenance of suppression of host defense in the tissue containing haustoria and infection hyphae. On the other hand, cell cycle and cell defense rescue transcripts are strongly accumulated in the sporulation area. This combined LCM-transcriptomic approach brings new insights on the molecular mechanisms underlying urediniospore formation in rust fungi.
Soil engineering
in vivo
: harnessing natural biogeochemical systems for sustainable, multi-functional engineering solutions
Authors: DeJong Jason T. , Soga Kenichi , Banwart Steven A. , Whalley W. Richard , Ginn Timothy R. , Nelson Douglas C. , Mortensen Brina M. , Martinez Brian C. , Barkouki Tammer
Published: September 2010

Carbon sequestration, infrastructure rehabilitation, brownfields clean-up, hazardous waste disposal, water resources protection and global warming—these twenty-first century challenges can neither be solved by the high-energy consumptive practices that hallmark industry today, nor by minor tweaking or optimization of these processes. A more radical, holistic approach is required to develop the sustainable solutions society needs. Most of the above challenges occur within, are supported on, are enabled by or grown from soil. Soil, contrary to conventional civil engineering thought, is a living system host to multiple simultaneous processes. It is proposed herein that ‘soil engineering
in vivo
’, wherein the natural capacity of soil as a living ecosystem is used to provide multiple solutions simultaneously, may provide new, innovative, sustainable solutions to some of these great challenges of the twenty-first century. This requires a multi-disciplinary perspective that embraces the science of biology, chemistry and physics and applies this knowledge to provide multi-functional civil and environmental engineering designs for the soil environment. For example, can native soil bacterial species moderate the carbonate cycle in soils to simultaneously solidify liquefiable soil, immobilize reactive heavy metals and sequester carbon—effectively providing civil engineering functionality while clarifying the ground water and removing carbon from the atmosphere? Exploration of these ideas has begun in earnest in recent years. This paper explores the potential, challenges and opportunities of this new field, and highlights one biogeochemical function of soil that has shown promise and is developing rapidly as a new technology. The example is used to propose a generalized approach in which the potential of this new field can be fully realized.
Sepsis with prolonged hypotension due to Moraxella osloensis in a non-immunocompromised child
Authors: Dien Bard Jennifer , Lewinski Michael , Summanen Paula H. , Deville Jaime G.
Published: September 2010

We report a case of septicaemia with prolonged, refractory hypotension related toMoraxella osloensisisolated in a non-immunocompromised paediatric patient.
Bactericidal effects of non-thermal argon plasma in vitro, in biofilms and in the animal model of infected wounds
Authors: Ermolaeva Svetlana A. , Varfolomeev Alexander F. , Chernukha Marina Yu. , Yurov Dmitry S. , Vasiliev Mikhail M. , Kaminskaya Anastasya A. , Moisenovich Mikhail M. , Romanova Julia M. , Murashev Arcady N. , Selezneva Irina I. , Shimizu Tetsuji , Sysolyatina Elena V. , Shaginyan Igor A. , Petrov Oleg F. , Mayevsky Evgeny I. , Fortov Vladimir E. , Morfill Gregor E. , Naroditsky Boris S. , Gintsburg Alexander L.
Published: September 2010

Non-thermal (low-temperature) physical plasma is under intensive study as an alternative approach to control superficial wound and skin infections when the effectiveness of chemical agents is weak due to natural pathogen or biofilm resistance. The purpose of this study was to test the individual susceptibility of pathogenic bacteria to non-thermal argon plasma and to measure the effectiveness of plasma treatments against bacteria in biofilms and on wound surfaces. Overall, Gram-negative bacteria were more susceptible to plasma treatment than Gram-positive bacteria. For the Gram-negative bacteriaPseudomonas aeruginosa,Burkholderia cenocepaciaandEscherichia coli, there were no survivors among the initial 105c.f.u. after a 5 min plasma treatment. The susceptibility of Gram-positive bacteria was species- and strain-specific.Streptococcus pyogeneswas the most resistant with 17 % survival of the initial 105c.f.u. after a 5 min plasma treatment.Staphylococcus aureushad a strain-dependent resistance with 0 and 10 % survival from 105c.f.u. of the Sa 78 and ATCC 6538 strains, respectively.Staphylococcus epidermidisandEnterococcus faeciumhad medium resistance. Non-ionized argon gas was not bactericidal. Biofilms partly protected bacteria, with the efficiency of protection dependent on biofilm thickness. Bacteria in deeper biofilm layers survived better after the plasma treatment. A rat model of a superficial slash wound infected withP. aeruginosaand the plasma-sensitiveStaphylococcus aureusstrain Sa 78 was used to assess the efficiency of argon plasma treatment. A 10 min treatment significantly reduced bacterial loads on the wound surface. A 5-day course of daily plasma treatments eliminatedP. aeruginosafrom the plasma-treated animals 2 days earlier than from the control ones. A statistically significant increase in the rate of wound closure was observed in plasma-treated animals after the third day of the course. Wound healing in plasma-treated animals slowed down after the course had been completed. Overall, the results show considerable potential for non-thermal argon plasma in eliminating pathogenic bacteria from biofilms and wound surfaces.
Interleukin-18-mediated enhancement of the protective effect of an infectious laryngotracheitis virus glycoprotein B plasmid DNA vaccine in chickens
Authors: Chen Hong-Ying , Zhang Hong-Ying , Li Xin-Sheng , Cui Bao-An , Wang Shu-Juan , Geng Jing-Wei , Li Kun
Published: September 2010

The immunogenicity of an infectious laryngotracheitis virus (ILTV) glycoprotein B (gB) plasmid DNA vaccine and the immunoregulatory activity of chicken interleukin-18 (IL-18) were investigated in a challenge model. Two recombinant plasmids, pcDNA3.1/gB (pgB) and pcDNA3.1/IL-18 (pIL-18), containing gB and IL-18 were constructed. Chickens were intramuscularly administered two immunizations 2 weeks apart, and challenged with the virulent CG strain of ILTV 2 weeks later. All animals vaccinated with pgB alone or with a combination of pgB plus pIL-18 developed a specific anti-ILTV ELISA antibody and splenocyte proliferation response. The ratios of CD4+ to CD8+ T lymphocytes in chickens immunized with pgB plus pIL-18 were significantly higher than in those immunized with pgB alone. Co-injection of pIL-18 significantly increased the production of gamma interferon and IL-2, indicating that IL-18 enhances the T helper 1-dominant immune response. Challenge experiments showed that the morbidity rate in the pgB group (25 %) was significantly higher than that in the pgB plus pIL-18 group (10 %). The mortality rates in the pgB and pgB plus pIL-18 groups were 10 and 0 %, respectively, and the corresponding protection rates were 60 and 80 %. These results indicate that IL-18 may be an effective adjuvant for an ILTV vaccine.
Heterologous expression of the surface-layer-like protein SllB induces the formation of long filaments of Escherichia coli consisting of protein-stabilized outer membrane
Authors: Lederer Franziska Linda , Günther Tobias Jan , Flemming Katrin , Raff Johannes , Fahmy Karim , Springer Armin , Pollmann Katrin
Published: September 2010

Escherichia coliis one of the best studied micro-organisms and is the most widely used host in genetic engineering. The Gram-negative single cells are rod-shaped, and filaments are usually not found. Here, we describe the reproducible formation of elongatedE. colicells. During heterologous expression of the silent surface (S)-layer protein genesllBfromLysinibacillus sphaericusJG-A12 inE. coliBL21(DE3), the cells were arranged as long chains which were surrounded by highly stable sheaths. These filaments had a length of >100 μm. In the stationary growth phase, microscopic analyses demonstrated the formation of unusually long transparent tube-like structures which were enclosing separate single cells. The tube-like structures were isolated and analysed by SDS-PAGE, infrared-spectroscopy and different microscopic methods in order to identify their unusual composition and structure. The tube-like structures were found to be like outer membranes, containing high levels of proteins and to which the recombinant S-layer proteins were attached. Despite the entire structure being indicative of a disordered cell division, the bacterial cells were highly viable and stable. To our knowledge, this is the first time that the induction of drastic morphological changes inE. coliby the expression of a foreign protein has been reported.
Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis
Authors: Roger Laure C. , McCartney Anne L.
Published: September 2010

From birth onwards, the gastrointestinal (GI) tract of infants progressively acquires a complex range of micro-organisms. It is thought that by 2 years of age the GI microbial population has stabilized. Within the developmental period of the infant GI microbiota, weaning is considered to be most critical, as the infant switches from a milk-based diet (breast and/or formula) to a variety of food components. Longitudinal analysis of the biological succession of the infant GI/faecal microbiota is lacking. In this study, faecal samples were obtained regularly from 14 infants from 1 month to 18 months of age. Seven of the infants (including a set of twins) were exclusively breast-fed and seven were exclusively formula-fed prior to weaning, with 175 and 154 faecal samples, respectively, obtained from each group. Diversity and dynamics of the infant faecal microbiota were analysed by using fluorescencein situhybridization and denaturing gradient gel electrophoresis. Overall, the data demonstrated large inter- and intra-individual differences in the faecal microbiological profiles during the study period. However, the infant faecal microbiota merged with time towards a climax community within and between feeding groups. Data from the twins showed the highest degree of similarity both quantitatively and qualitatively. Inter-individual variation was evident within the infant faecal microbiota and its development, even within exclusively formula-fed infants receiving the same diet. These data can be of help to future clinical trials (e.g. targeted weaning products) to organize protocols and obtain a more accurate outline of the changes and dynamics of the infant GI microbiota.
Intestinal lactobacilli and the DC-SIGN gene for their recognition by dendritic cells play a role in the aetiology of allergic manifestations
Authors: Penders John , Thijs Carel , Mommers Monique , Stobberingh Ellen E. , Dompeling Edward , Reijmerink Naomi E. , van den Brandt Piet A. , Kerkhof Marjan , Koppelman Gerard H. , Postma Dirkje S.
Published: September 2010

Diminished exposure to harmless micro-organisms, such as lactobacilli, has been suggested to play a role in the increased prevalence of allergic disorders in Westernized communities. The development of allergies depends on both environmental factors and genetic variations, including polymorphisms in genes encoding pattern recognition receptors. The present study examines the effects of both colonization with specificLactobacillusspecies and genetic variations in DC-SIGN, a pattern recognition receptor on dendritic cells that recognizes lactobacilli, on the development of atopic dermatitis (AD) and sensitization in infancy. Within the KOALA Birth Cohort Study, faecal samples of 681 one-month-old infants were collected and quantitatively screened for fiveLactobacillusspecies:L. casei,L. paracasei,L. rhamnosus,L. acidophilusandL. reuteri. Eleven haplotype-tagging polymorphisms in theDC-SIGNgene were genotyped in these children. Allergic outcomes were a clinical diagnosis of AD and sensitization (specific IgE) at age 2 years.L. rhamnosus(31.5 %),L. paracasei(31.3 %) andL. acidophilus(14.4 %) were frequently detected in the faecal samples of one-month-old infants, whereasL. casei(2.5 %) andL. reuteri(<1 %) were rare. Colonization withL. paracaseidecreased the risk of AD significantly (odds ratio 0.57, 95 % confidence interval 0.32–0.99), whereas effects ofL. acidophiluswere of borderline statistical significance (0.46, 0.20–1.04). TwoDC-SIGNpolymorphisms, rs11465413 and rs8112555, were statistically significantly associated with atopic sensitization. The present study supports the ‘old friends’ hypothesis suggesting that certain health-beneficial micro-organisms protect us from developing allergies and that these protective effects are species-dependent. Firm conclusions on the potential interaction between lactobacillus colonization and genetic variations inDC-SIGNin association with the development of allergic disorders cannot be drawn, given the limited power of our study. Therefore, incorporation of consecutive faecal sampling in newly started (birth) cohort studies would be a first requisite to further increase our understanding of host–microbial interactions in health and disease.