Pl2 resistance gene differentiates the pathogenicity in four "Plasmopara halstedii" (sunflower downy mildew) races 304, 704, 314 and 714

In order to clarify the role of Pl2 resistance gene in differentiation the pathogenicity in Plasmopara halstedii (sunflower downy mildew), analyses were carried out in four pathotypes: isolates of races 304 and 314 that do not overcome Pl2 gene, and isolates of races 704 and 714 that can overcome Pl2 gene. Based on the reaction for the P. halstedii isolates to sunflower hybrids varying only in Pl resistance genes, isolates of races 704 and 714 were more virulent than isolates of races 304 and 314. Index of aggressiveness was calculated for pathogen isolates and revealed the presence of significant differences between isolates of races 304 and 314 (more aggressive) and isolates of races 704 and 714 (less aggressive). There were morphological and genetic variations for the four P. halstedii isolates without a correlation with pathogenic diversity. The importance of the Pl2 resistance gene to differentiate the pathogenicity in sunflower downy mildew was discussed.

Within-Otolith Variability in Chemical Fingerprints: Implications for Sampling Designs and Possible Environmental Interpretation

Largely used as a natural biological tag in studies of dispersal/connectivity of fish, otolith elemental fingerprinting is usually analyzed by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). LA-ICP-MS produces an elemental fingerprint at a discrete time-point in the life of a fish and can generate data on within-otolith variability of that fingerprint. The presence of within-otolith variability has been previously acknowledged but not incorporated into experimental designs on the presumed, but untested, grounds of both its negligibility compared to among-otolith variability and of spatial autocorrelation among multiple ablations within an otolith. Here, using a hierarchical sampling design of spatial variation at multiple scales in otolith chemical fingerprints for two Mediterranean coastal fishes, we explore: 1) whether multiple ablations within an otolith can be used as independent replicates for significance tests among otoliths, and 2) the implications of incorporating within-otolith variability when assessing spatial variability in otolith chemistry at a hierarchy of spatial scales (different fish, from different sites, at different locations on the Apulian Adriatic coast). We find that multiple ablations along the same daily rings do not necessarily exhibit spatial dependency within the otolith and can be used to estimate residual variability in a hierarchical sampling design. Inclusion of within-otolith measurements reveals that individuals at the same site can show significant variability in elemental uptake. Within-otolith variability examined across the spatial hierarchy identifies differences between the two fish species investigated, and this finding leads to discussion of the potential for within-otolith variability to be used as a marker for fish exposure to stressful conditions. We also demonstrate that a 'cost'-optimal allocation of sampling effort should typically include some level of within-otolith replication in the experimental design. Our findings provide novel evidence to aid the design of future sampling programs and improve our general understanding of the mechanisms regulating elemental fingerprints.

Bandstructure approach to near edge structure

We review the current state of the art in EELS fingerprinting by computer simulation, focusing on the bandstructure approach to the problem. Currently calculations are made using a one electron theory, but we describe in principle the way to go beyond this to include final state effects. We include these effects within the one electron framework using the Slater transition state formula and assess the errors involved. Two examples are then given which illustrate the use of the one electron approximation within density functional theory. Our approach is to combine predicted atomic structure with predicted electronic structure to assist in fingerprinting of complex crystal structures.

Chromosomal rearrangements affecting biofilm production and antibiotic resistance in a Staphylococcus epidermidis strain causing shunt-associated ventriculitis.

Ziebuhr W, Dietrich K, Trautmann M, Wilhelm M. Institut für Molekulare Infektionsbiologie, Würzburg, Germany. w.ziebuhr@mail.uni-wuerzburg.de During two clinical courses of shunt-associated meningitis in a 3-month-old child, five multiresistant S. epidermidis isolates were obtained and analyzed with regard to biofilm production and antibiotic susceptibility. Three S. epidermidis strains, which were initially isolated from the cerebrospinal fluid, produced biofilms on polystyrene tissue culture plates. Following antibiotic treatment and subsequent exchange of the shunt system, sterilization of the CSF was achieved. However, after three weeks a relapse of the infection occurred. The two S. epidermidis isolates obtained now were biofilm negative, but showed an identical resistance pattern as those from the previous infection, except that resistance to rifampicin and increased mininal inhibitory concentrations of aminoglycoside antibiotics had emerged. DNA fingerprinting by PFGE indicated the clonal origin of all isolates. However, some DNA rearrangements and differences in the IS256-specific hybridization patterns could be identified in the isolates from the second infection period that led to altered biofilm formation and increased expression of aminoglycoside resistance traits. The data evidence that variation of biofilm expression occurs in vivo during an infection and highlight the extraordinary genome flexibility of pathogenic S. epidermidis.

Metamaterials Nanosensor for Label-free Analysis of Conformation and Molecular Interaction of Biomolecules

Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding of their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g. G-quadruplexes, in different environments (Fig. 1). We further demonstrate the use of the metamaterials for fingerprinting and detection of arginine-glycine-glycine domain of nucleolin, a cancer biomarker which specifically binds to a G-quadruplex, with the picomolar sensitivity. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays.

Label-free Analysis of Conformational Dynamics and Molecular Interaction of Biomolecules by Vis-NIR Metasensor

Analysis of binding recognition and conformation of biomolecules is of paramount important in understanding of their vital functions in complex biological systems. By enabling sub-wavelength light localization and strong local field enhancement, plasmonic biosensors have become dominant tools used for such analysis owing to their label-free and real-time attributes1,2. However, the plasmonic biosensors are not well-suited to provide information regarding conformation or chemical fingerprint of biomolecules. Here, we show that plasmonic metamaterials, consisting of periodic arrays of artificial split-ring resonators (SRRs)3, can enable capabilities of both sensing and fingerprinting of biomolecules. We demonstrate that by engineering geometry of individual SRRs, localized surface plasmon resonance (LSPR) frequency of the metamaterials could be tuned to visible-near infrared regimes (Vis-NIR) such that they possess high local field enhancement for surface-enhanced Raman scattering spectroscopy (SERS). This will provide the basis for the development of a dual mode label-free conformational-resolving and quantitative detection platform. We present here the ability of each sensing mode to independently detect binding adsorption and to identify different conformational states of Guanine (G)-rich DNA monolayers in different environment milieu. Also shown is the use of the nanosensor for fingerprinting and detection of Arginine-Glycine-Glycine (RGG) peptide binding to the G-quadruplex aptamer. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays that the conventional, population-averaged plasmonic biosensors cannot achieve.

Metamaterials-Based Label-Free Nanosensor for Conformation and Affinity Biosensing

Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding of their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that highly tunable plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g. G-quadruplexes, in different environments. We further demonstrate the use of the metamaterials for fingerprinting and detection of arginine-glycine-glycine domain of nucleolin, a cancer biomarker which specifically binds to a G-quadruplex, with the picomolar sensitivity.

Early Holocene M similar to 6 explosive eruption from Plosky volcanic massif (Kamchatka) and its tephra as a link between terrestrial and marine paleoenvironmental records

We report tephrochronological and geochemical data on early Holocene activity from Plosky volcanic massif in the Kliuchevskoi volcanic group, Kamchatka Peninsula. Explosive activity of this volcano lasted for similar to 1.5 kyr, produced a series of widely dispersed tephra layers, and was followed by profuse low-viscosity lava flows. This eruptive episode started a major reorganization of the volcanic structures in the western part of the Kliuchevskoi volcanic group. An explosive eruption from Plosky (M similar to 6), previously unstudied, produced tephra (coded PL2) of a volume of 10-12 km(3) (11-13 Gt), being one of the largest Holocene explosive eruptions in Kamchatka. Characteristic diagnostic features of the PL2 tephra are predominantly vitric sponge-shaped fragments with rare phenocrysts and microlites of plagioclase, olivine and pyroxenes, medium- to high-K basaltic andesitic bulk composition, high-K, high-Al and high-P trachyandesitic glass composition with SiO2 = 57.5-59.5 wt%, K2O = 2.3-2.7 wt%, Al2O3 = 15.8-16.5 wt%, and P2O5 = 0.5-0.7 wt%. Other diagnostic features include a typical subduction-related pattern of incompatible elements, high concentrations of all REE (> 10x mantle values), moderate enrichment in LREE (La/Yb similar to 5.3), and non-fractionated mantle-like pattern of LILE. Geochemical fingerprinting of the PL2 tephra with the help of EMP and LA-ICP-MS analyses allowed us to map its occurrence in terrestrial sections across Kamchatka and to identify this layer in Bering Sea sediment cores at a distance of > 600 km from the source. New high-precision C-14 dates suggest that the PL2 eruption occurred similar to 10,200 cal BP, which makes it a valuable isochrone for early Holocene climate fluctuations and permits direct links between terrestrial and marine paleoenvironmental records. The terrestrial and marine C-14 dates related to the PL2 tephra have allowed us to estimate an early Holocene reservoir age for the western Bering Sea at 1,410 +/- A 64 C-14 years. Another important tephra from the early Holocene eruptive episode of Plosky volcano, coded PL1, was dated at 11,650 cal BP. This marker is the oldest geochemically characterized and dated tephra marker layer in Kamchatka to date and is an important local marker for the Younger Dryas-early Holocene transition. One more tephra from Plosky, coded PL3, can be used as a marker northeast of the source at a distance of similar to 110 km.

Evaluation of methodologies to determine vegetable oil species present in oil mixtures: Proposition of an approach to meet the EU legislation demands for correct vegetable oils labelling

Refined vegetable oils are widely used in the food industry as ingredients or components in many processed food products in the form of oil blends. To date, the generic term 'vegetable oil' has been used in the labelling of food containing oil blends. With the introduction of new EU Regulation for Food Information (1169/2011) due to take effect in 2014, the oil species used must be clearly identified on the package and there is a need for development of fit for purpose methodology for industry and regulators alike to verify the oil species present in a product. The available methodologies that may be employed to authenticate the botanical origin of a vegetable oil admixture were reviewed and evaluated. The majority of the sources however, described techniques applied to crude vegetable oils such as olive oil due to the lack of refined vegetable oil focused studies. Nevertheless, DNA based typing methods and stable isotopes procedures were found not suitable for this particular purpose due to several issues. Only a small number of specific chromatographic and spectroscopic fingerprinting methods in either targeted or untargeted mode were found to be applicable in potentially providing a solution to this complex authenticity problem. Applied as a single method in isolation, these techniques would be able to give limited information on the oils identity as signals obtained for various oil types may well be overlapping. Therefore, more complex and combined approaches are likely to be needed to identify the oil species present in oil blends employing a stepwise approach in combination with advanced chemometrics. Options to provide such a methodology are outlined in the current study.

The electrochemical reduction of 1-bromo-4-nitrobenzene at zinc electrodes in a room-temperature ionic liquid: a facile route for the formation of arylzinc compounds

The electrochemical reduction of 1-bromo-4-nitrobenzene (p-BrC₆H₄NO₂) at zinc microelectrodes in the [C(₄)mPyrr][NTf₂] ionic liquid was investigated via cyclic voltammetry. The reduction was found to occur via an EC type mechanism, where p-BrC₆H₄NO₂ is first reduced by one electron, quasi-reversibly, to yield the corresponding radical anion. The radical anions then react with the Zn electrode to form arylzinc products. Introduction of carbon dioxide into the system led to reaction with the arylzinc species, fingerprinting the formation of the latter. This method thus demonstrates a proof-of-concept of the formation of functionalised arylzinc species.

Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis

Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.

A LEED STRUCTURAL STUDY OF THE CO INDUCED RECONSTRUCTION OF PD(110) - EVIDENCE FOR A MISSING ROW STRUCTURE

Molecularly adsorbed CO on Pd{110} has been shown (R. Raval et al., Chem. Phys. Lett. 167 (1990) 391, ref. [1]) to induce a substantial reconstruction of the surface in the coverage range 0.3 <theta less-than-or-equal-to 0.75. Throughout this coverage range, the adsorbate-covered reconstructed surface exhibits a (4 x 2) LEED pattern. However, the exact nature of the reconstruction remains uncertain. We have conducted a LEED I(E) "fingerprinting" analysis of the CO/Pd{110}-(4 x 2) structure in order to establish the type of reconstruction induced in the metal surface. This study shows that the LEED I(E) profiles of the integral order and appropriate half-order beams of the CO/Pd{110}-(4 x 2) pattern closely resemble the I(E) profiles theoretically calculated for a Pd{110}-(1 x 2) missing-row structure. Additionally, there is a strong resemblance to the experimental LEED I(E) profiles for the Cs/Pd{110}-(1 x 2) structure which has also been shown to exhibit the missing-row structure. On the basis of this evidence we conclude that the CO/Pd{110}-(4 x 2) LEED pattern arises from a missing-row reconstruction of the Pd{110} surface which gives rise to a strong underlying (1 x 2) pattern plus a poorly ordered CO overlayer which produces weak, diffuse fourth-order spots in the LEED pattern.

Cooperative positioning for heterogeneous wireless systems

Future emerging market trends head towards positioning based services placing a new perspective on the way we obtain and exploit positioning information. On one hand, innovations in information technology and wireless communication systems enabled the development of numerous location based applications such as vehicle navigation and tracking, sensor networks applications, home automation, asset management, security and context aware location services. On the other hand, wireless networks themselves may bene t from localization information to improve the performances of di erent network layers. Location based routing, synchronization, interference cancellation are prime examples of applications where location information can be useful. Typical positioning solutions rely on measurements and exploitation of distance dependent signal metrics, such as the received signal strength, time of arrival or angle of arrival. They are cheaper and easier to implement than the dedicated positioning systems based on ngerprinting, but at the cost of accuracy. Therefore intelligent localization algorithms and signal processing techniques have to be applied to mitigate the lack of accuracy in distance estimates. Cooperation between nodes is used in cases where conventional positioning techniques do not perform well due to lack of existing infrastructure, or obstructed indoor environment. The objective is to concentrate on hybrid architecture where some nodes have points of attachment to an infrastructure, and simultaneously are interconnected via short-range ad hoc links. The availability of more capable handsets enables more innovative scenarios that take advantage of multiple radio access networks as well as peer-to-peer links for positioning. Link selection is used to optimize the tradeo between the power consumption of participating nodes and the quality of target localization. The Geometric Dilution of Precision and the Cramer-Rao Lower Bound can be used as criteria for choosing the appropriate set of anchor nodes and corresponding measurements before attempting location estimation itself. This work analyzes the existing solutions for node selection in order to improve localization performance, and proposes a novel method based on utility functions. The proposed method is then extended to mobile and heterogeneous environments. Simulations have been carried out, as well as evaluation with real measurement data. In addition, some speci c cases have been considered, such as localization in ill-conditioned scenarios and the use of negative information. The proposed approaches have shown to enhance estimation accuracy, whilst signi cantly reducing complexity, power consumption and signalling overhead.

Identificação de indicadores moleculares de bem-estar durante o cultivo de dourada (Sparus aurata, Linnaeus 1758), utilizando técnicas de proteómica

Dissertação de Mestrado, Biologia Marinha, Especialização em Biotecnologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2008