Genotyping Vitis vinifera L. cultivars of Cyprus by microsatellite analysis

Twelve native Vitis vinifera L. cultivars of Cyprus were genotyped at 11 highly polymorphic microsatellite markers. The obtained microsatellite allelic profiles allowed precise identification and discrimination of all tested cultivars. Each cultivar had a unique allelic profile. The low PI value (5.1 x 10-9) demonstrated the high descriptive power of the chosen markers for the investigated set of grapevines. Three cases of synonymy of Cyprus cultivars with cultivars grown in other countries under different names were verified: (1) Cyprus Malaga and Muscat of Alexandria, (2) Cyprus Lefkas and Greek Verdzami, and (3) Cyprus Moscato, Bulgarian Tamyanka and Italian Moscato Bianco. The homonymy of Cyprus Sideritis and Greek Sideritis as well as of Cyprus Mavro and Bulgarian Mavrud was shown not to rely on genetic similarity.

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Impact of catalyst layer morphology on the operation of high temperature PEM fuel cells

Electrochemical impedance spectroscopy (EIS) is a well-established method to analyze a polymer electrolyte membrane fuel cell (PEMFC). However, without further data processing, the impedance spectrum yields only qualitative insight into the mechanism and individual contribution of transport, kinetics, and ohmic losses to the overall fuel cell limitations. The distribution of relaxation times (DRT) method allows quantifying each of these polarization losses and evaluates their contribution to a given electrocatalyst\u27s depreciated performances. We coupled this method with a detailed morphology study to investigate the impact of the 3D-structure on the processes occurring inside a high-temperature polymer electrolyte membrane fuel cell (HT-PEMFC). We tested a platinum catalyst (Pt/C), a platinum-cobalt alloy catalyst (Pt$_{3}$Co/C), and a platinum group metal-free iron-nitrogen-carbon (Fe–N–C) catalyst. We found that the hampered mass transport in the latter is mainly responsible for its low performance in the MEA (along with its decreased intrinsic performances for the ORR reaction). The better performance of the alloy catalyst can be explained by both improved mass transport and a lower ORR resistance. Furthermore, single-cell tests show that the catalyst layer morphology influences the distribution of phosphoric acid during conditioning

Increased power generation in supercapacitive microbial fuel cell stack using Fe-N-C cathode catalyst

The anode and cathode electrodes of a microbial fuel cell (MFC) stack, composed of 28 single MFCs, were used as the negative and positive electrodes, respectively of an internal self-charged supercapacitor. Particularly, carbon veil was used as the negative electrode and activated carbon with a Fe-based catalyst as the positive electrode. The red-ox reactions on the anode and cathode, self-charged these electrodes creating an internal electrochemical double layer capacitor. Galvanostatic discharges were performed at different current and time pulses. Supercapacitive-MFC (SC-MFC) was also tested at four different solution conductivities. SC-MFC had an equivalent series resistance (ESR) decreasing from 6.00 Ω to 3.42 Ω in four solutions with conductivity between 2.5 mScm−1 and 40 mScm−1. The ohmic resistance of the positive electrode corresponded to 75–80% of the overall ESR. The highest performance was achieved with a solution conductivity of 40 mS cm−1 and this was due to the positive electrode potential enhancement for the utilization of Fe-based catalysts. Maximum power was 36.9mW (36.9Wm−3) that decreased with increasing pulse time. SC-MFC was subjected to 4520 cycles (8 days) with a pulse time of 5 s (ipulse 55 mA) and a self-recharging time of 150 s showing robust reproducibility

Tissue-specific modulation of gene expression in response to lowered insulin signalling in Drosophila

Reduced activity of the insulin/IGF signalling network increases health during ageing in multiple species. Diverse and tissue-specific mechanisms drive the health improvement. Here, we performed tissue-specific transcriptional and proteomic profiling of long-lived Drosophila dilp2-3,5 mutants, and identified tissue-specific regulation of >3600 transcripts and >3700 proteins. Most expression changes were regulated post-transcriptionally in the fat body, and only in mutants infected with the endosymbiotic bacteria, Wolbachia pipientis, which increases their lifespan. Bioinformatic analysis identified reduced co-translational ER targeting of secreted and membrane-associated proteins and increased DNA damage/repair response proteins. Accordingly, age-related DNA damage and genome instability were lower in fat body of the mutant, and overexpression of a minichromosome maintenance protein subunit extended lifespan. Proteins involved in carbohydrate metabolism showed altered expression in the mutant intestine, and gut-specific overexpression of a lysosomal mannosidase increased autophagy, gut homeostasis, and lifespan. These processes are candidates for combatting ageing-related decline in other organisms

LHC Optics Measurement with Proton Tracks Detected by the Roman Pots of the TOTEM Experiment

Precise knowledge of the beam optics at the LHC is crucial to fulfil the physics goals of the TOTEM experiment, where the kinematics of the scattered protons is reconstructed with the near-beam telescopes -- so-called Roman Pots (RP). Before being detected, the protons' trajectories are influenced by the magnetic fields of the accelerator lattice. Thus precise understanding of the proton transport is of key importance for the experiment. A novel method of optics evaluation is proposed which exploits kinematical distributions of elastically scattered protons observed in the RPs. Theoretical predictions, as well as Monte Carlo studies, show that the residual uncertainty of this optics estimation method is smaller than 0.25 percent.Comment: 20 pages, 11 figures, 5 figures, to be submitted to New J. Phy

Double diffractive cross-section measurement in the forward region at LHC

The first double diffractive cross-section measurement in the very forward region has been carried out by the TOTEM experiment at the LHC with center-of-mass energy of sqrt(s)=7 TeV. By utilizing the very forward TOTEM tracking detectors T1 and T2, which extend up to |eta|=6.5, a clean sample of double diffractive pp events was extracted. From these events, we measured the cross-section sigma_DD =(116 +- 25) mub for events where both diffractive systems have 4.7 <|eta|_min < 6.5 .Comment: 5 pages, 1 figure, submitted for publicatio

Performance of the TOTEM Detectors at the LHC

The TOTEM Experiment is designed to measure the total proton-proton cross-section with the luminosity-independent method and to study elastic and diffractive pp scattering at the LHC. To achieve optimum forward coverage for charged particles emitted by the pp collisions in the interaction point IP5, two tracking telescopes, T1 and T2, are installed on each side of the IP in the pseudorapidity region 3.1 < = |eta | < = 6.5, and special movable beam-pipe insertions - called Roman Pots (RP) - are placed at distances of +- 147 m and +- 220 m from IP5. This article describes in detail the working of the TOTEM detector to produce physics results in the first three years of operation and data taking at the LHC.Comment: 40 pages, 31 figures, submitted to Int. J. Mod. Phys.

Diamond Detectors for the TOTEM Timing Upgrade

This paper describes the design and the performance of the timing detector developed by the TOTEM Collaboration for the Roman Pots (RPs) to measure the Time-Of-Flight (TOF) of the protons produced in central diffractive interactions at the LHC. The measurement of the TOF of the protons allows the determination of the longitudinal position of the proton interaction vertex and its association with one of the vertices reconstructed by the CMS detectors. The TOF detector is based on single crystal Chemical Vapor Deposition (scCVD) diamond plates and is designed to measure the protons TOF with about 50 ps time precision. This upgrade to the TOTEM apparatus will be used in the LHC run 2 and will tag the central diffractive events up to an interaction pileup of about 1. A dedicated fast and low noise electronics for the signal amplification has been developed. The digitization of the diamond signal is performed by sampling the waveform. After introducing the physics studies that will most profit from the addition of these new detectors, we discuss in detail the optimization and the performance of the first TOF detector installed in the LHC in November 2015.Comment: 26 pages, 18 figures, 2 tables, submitted for publication to JINS