Enhanced susceptibility of Candida albicans to chlorhexidine under anoxia

Aim: Periodontal pockets can be colonized not only by bacteria, but also by Candida albicans. However, its role in periodontitis is unknown. This study evaluated the inhibitory performance of chlorhexidine digluconate under normoxic and anoxic conditions against 16 strains of C. albicans from periodontal pockets and other 20 from the oral mucosa. Methods: Strains were grown in normoxia and anoxia to adapt themselves to the different atmospheric conditions. Microdilution-based assays were carried out to determine the minimum concentrations of chlorhexidine that may restrain the conditioned candidal strains, in normoxia (normoxic MIC) and anoxia (anoxic MIC). The Mann-Whitney U test was used to evaluate the antimicrobial effect of chlorhexidine on C. albicans under normoxic and anoxic conditions (α = 0.05). Results: The normoxic MIC of chlorhexidine varied broadly from 150 to 1200 μg/mL, whereas its anoxic MIC varied narrower from 2.34 to 37.5 μg/mL. Regarding the origins of strains, no statistically significant differences (p > 0.05) were found. Conclusions: These results indicate that anoxic environmental conditions, compatible with periodontal pockets, tend to enhance C. albicans susceptibility to chlorhexidine.published_or_final_versio

A framework for automated enrichment of functionally significant inverted repeats in whole genomes

<p>Abstract</p> <p>Background</p> <p>RNA transcripts from genomic sequences showing dyad symmetry typically adopt hairpin-like, cloverleaf, or similar structures that act as recognition sites for proteins. Such structures often are the precursors of non-coding RNA (ncRNA) sequences like microRNA (miRNA) and small-interfering RNA (siRNA) that have recently garnered more functional significance than in the past. Genomic DNA contains hundreds of thousands of such inverted repeats (IRs) with varying degrees of symmetry. But by collecting statistically significant information from a known set of ncRNA, we can sort these IRs into those that are likely to be functional.</p> <p>Results</p> <p>A novel method was developed to scan genomic DNA for partially symmetric inverted repeats and the resulting set was further refined to match miRNA precursors (pre-miRNA) with respect to their density of symmetry, statistical probability of the symmetry, length of stems in the predicted hairpin secondary structure, and the GC content of the stems. This method was applied on the <it>Arabidopsis thaliana</it> genome and validated against the set of 190 known Arabidopsis pre-miRNA in the miRBase database. A preliminary scan for IRs identified 186 of the known pre-miRNA but with 714700 pre-miRNA candidates. This large number of IRs was further refined to 483908 candidates with 183 pre-miRNA identified and further still to 165371 candidates with 171 pre-miRNA identified (i.e. with 90% of the known pre-miRNA retained).</p> <p>Conclusions</p> <p>165371 candidates for potentially functional miRNA is still too large a set to warrant wet lab analyses, such as northern blotting, on all of them. Hence additional filters are needed to further refine the number of candidates while still retaining most of the known miRNA. These include detection of promoters and terminators, homology analyses, location of candidate relative to coding regions, and better secondary structure prediction algorithms. The software developed is designed to easily accommodate such additional filters with a minimal experience in Perl.</p

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments

Attractor dynamics approach to joint transportation by autonomous robots: theory, implementation and validation on the factory floor

This paper shows how non-linear attractor dynamics can be used to control teams of two autonomous mobile robots that coordinate their motion in order to transport large payloads in unknown environments, which might change over time and may include narrow passages, corners and sharp U-turns. Each robot generates its collision-free motion online as the sensed information changes. The control architecture for each robot is formalized as a non-linear dynamical system, where by design attractor states, i.e. asymptotically stable states, dominate and evolve over time. Implementation details are provided, and it is further shown that odometry or calibration errors are of no significance. Results demonstrate flexible and stable behavior in different circumstances: when the payload is of different sizes; when the layout of the environment changes from one run to another; when the environment is dynamice.g. following moving targets and avoiding moving obstacles; and when abrupt disturbances challenge team behavior during the execution of the joint transportation task.- This work was supported by FCT-Fundacao para a Ciencia e Tecnologia within the scope of the Project PEst-UID/CEC/00319/2013 and by the Ph.D. Grants SFRH/BD/38885/2007 and SFRH/BPD/71874/2010, as well as funding from FP6-IST2 EU-IP Project JAST (Proj. Nr. 003747). We would like to thank the anonymous reviewers, whose comments have contributed to improve the paper

Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions

Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal