Evaluation of a new high-throughput method for identifying quorum quenching bacteria

Quorum sensing (QS) is a population-dependent mechanism for bacteria to synchronize social behaviors such as secretion of virulence factors. The enzymatic interruption of QS, termed quorum quenching (QQ), has been suggested as a promising alternative anti-virulence approach. In order to efficiently identify QQ bacteria, we developed a simple, sensitive and high-throughput method based on the biosensor Agrobacterium tumefaciens A136. This method effectively eliminates false positives caused by inhibition of growth of biosensor A136 and alkaline hydrolysis of N-acylhomoserine lactones (AHLs), through normalization of beta-galactosidase activities and addition of PIPES buffer, respectively. Our novel approach was successfully applied in identifying QQ bacteria among 366 strains and 25 QQ strains belonging to 14 species were obtained. Further experiments revealed that the QQ strains differed widely in terms of the type ofQQenzyme, substrate specificity and heat resistance. The QQ bacteria identified could possibly be used to control disease in aquaculture

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Background: Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth ("deep sequencing"), low frequency variants can be detected. Here we present QQ-SNV (http://sourceforge.net/projects/qqsnv), a logistic regression classifier model developed for the Illumina sequencing platforms that uses the quantiles of the quality scores, to distinguish true single nucleotide variants from sequencing errors based on the estimated SNV probability. To train the model, we created a dataset of an in silico mixture of five HIV-1 plasmids. Testing of our method in comparison to the existing methods LoFreq, ShoRAH, and V-Phaser 2 was performed on two HIV and four HCV plasmid mixture datasets and one influenza H1N1 clinical dataset. Results: For default application of QQ-SNV, variants were called using a SNV probability cutoff of 0.5 (QQ-SNVD). To improve the sensitivity we used a SNV probability cutoff of 0.0001 (QQ-SNVHS). To also increase specificity, SNVs called were overruled when their frequency was below the 80th percentile calculated on the distribution of error frequencies (QQ-SNVHS-P80). When comparing QQ-SNV versus the other methods on the plasmid mixture test sets, QQ-SNVD performed similarly to the existing approaches. QQ-SNVHS was more sensitive on all test sets but with more false positives. QQ-SNVHS-P80 was found to be the most accurate method over all test sets by balancing sensitivity and specificity. When applied to a paired-end HCV sequencing study, with lowest spiked-in true frequency of 0.5 %, QQ-SNVHS-P80 revealed a sensitivity of 100 % (vs. 40-60 % for the existing methods) and a specificity of 100 % (vs. 98.0-99.7 % for the existing methods). In addition, QQ-SNV required the least overall computation time to process the test sets. Finally, when testing on a clinical sample, four putative true variants with frequency below 0.5 % were consistently detected by QQ-SNVHS-P80 from different generations of Illumina sequencers. Conclusions: We developed and successfully evaluated a novel method, called QQ-SNV, for highly efficient single nucleotide variant calling on Illumina deep sequencing virology data

Global descent obstructions for varieties

We show how to transport descent obstructions from the category of covers to the category of varieties. We deduce examples of curves having \QQ as field of moduli, that admit models over every completion of \QQ, but have no model over \QQ

qq' -> qq': a second look at the IR divergences

The transport properties of the quark-gluon plasma is important both from the point of view of the astrophysical systems and the heavy ion collisions. Therefore, accurate calculations of the elastic scattering cross-sections of $qq' \to qq'$ and q\qbar' \to q\qbar' processes are required. At the tree-diagram level exchange of massless gluons leads to divergent cross sections for such processes. An effective way to remove the infrared divergence is to introduce a Debye mass as an infrared regulator into the gluon propagator for the thermal gluons. In this work we find that at the two-gluon exchange level such a technique fails to remove the divergences. In a chiral symmetry broken phase the mass could be introduced following the standard procedure which cures the divergence. But in a chirally symmetric phase chiral invariant mass of the fermions needs to be considered.Comment: 4 pages, latex, 1 figur

Charm quark effects on the strong coupling extracted from the static force

We compute the fermionic contribution to the strong coupling $\alpha_{qq}$ extracted from the static force in Lattice QCD up to order $g^4$ in perturbation theory. This allows us to subtract the leading fermionic lattice artifacts from recent determinations of $\alpha_{qq}$ produced in simulations of two dynamical charm quarks. Moreover, by using a suitable parametrization of the $\beta_{qq}$-function, we can evaluate the charm loop effects on $\alpha_{qq}$ in the continuum limit.Comment: 8 pages, 2 figures; Proceedings of the 35th International Symposium on Lattice Field Theory, Granada, Spai

Exotic QQqˉqˉQQ\bar{q}\bar{q}, QQqˉsˉQQ\bar{q}\bar{s} and QQsˉsˉQQ\bar{s}\bar{s} states

After constructing the possible $J^P=0^-, 0^+, 1^-$ and $1^+$ $QQ\bar{q}\bar{q}$ tetraquark interpolating currents in a systematic way, we investigate the two-point correlation functions and extract the corresponding masses with the QCD sum rule approach. We study the $QQ\bar{q}\bar{q}$, $QQ\bar{q}\bar{s}$ and $QQ\bar{s}\bar{s}$ systems with various isospins $I=0, 1/2, 1$. Our numerical analysis indicates that the masses of doubly-bottomed tetraquark states are below the threshold of the two bottom mesons, two bottom baryons and one doubly bottomed baryon plus one anti-nucleon. Very probably these doubly-bottomed tetraquark states are stable.Comment: 37 pages, 2 figure

QCD color interactions between two quarks

We study the QCD color interactions between static two heavy quarks at zero temperature in a quenched SU(3) lattice gauge simulation: in addition to the standard singlet $q\bar{q}$ potentials, we calculate octet $q\bar{q}$ potentials, symmetric and antisymmetric $qq$ potentials. It is shown that the antisymmetric $qq$ channel behaves as a linearly rising potential at large quark separations. We further find that the $q\bar{q}$ octet and $qq$ symmetric channels have the complex dependence on the distance; at short distances they are repulsive forces, while at large distances, they show linearly rising feature. Ratio of string tensions between $q\bar{q}$ singlet and $qq$ antisymmetric potentials is described in terms of the Casimir factor