Rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae produces multiple DSF-family signals in regulation of virulence factor production

<p>Abstract</p> <p>Background</p> <p><it>Xanthomonas </it><it>oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>) is the causal agent of rice bacterial blight disease. <it>Xoo </it>produces a range of virulence factors, including EPS, extracellular enzyme, iron-chelating siderophores, and type III-secretion dependent effectors, which are collectively essential for virulence. Genetic and genomics evidence suggest that <it>Xoo </it>might use the diffusible signal factor (DSF) type quorum sensing (QS) system to regulate the virulence factor production. However, little is known about the chemical structure of the DSF-like signal(s) produced by <it>Xoo </it>and the factors influencing the signal production.</p> <p>Results</p> <p><it>Xoo </it>genome harbours an <it>rpf </it>cluster comprising <it>rpfB</it>, <it>rpfF</it>, <it>rpfC </it>and <it>rpfG</it>. The proteins encoded by these genes are highly homologous to their counterparts in <it>X. campestris </it>pv. <it>campestris </it>(<it>Xcc</it>), suggesting that <it>Xcc </it>and <it>Xoo </it>might use similar mechanisms for DSF biosynthesis and autoregulation. Consistent with <it>in silico </it>analysis, the <it>rpfF </it>mutant was DSF-deficient and the <it>rpfC </it>mutant produced about 25 times higher DSF-like activity than the wild type <it>Xoo </it>strain KACC10331. From the supernatants of <it>rpfC </it>mutant, we purified three compounds showing strong DSF-like activity. Mass spectrometry and NMR analysis revealed that two of them were the previously characterized DSF and BDSF; the third one was a novel unsaturated fatty acid with 2 double bonds and was designated as CDSF in this study. Further analysis showed that all the three DSF-family signals were synthesized via the enzyme RpfF encoded by <it>Xoo2868</it>. DSF and BDSF at a final concentration of 3 μM to the <it>rpfF </it>mutant could fully restore its extracellular xylanase activity and EPS production to the wild type level, but CDSF was less active than DSF and BDSF in induction of EPS and xylanase. DSF and CDSF shared a similar cell density-dependent production time course with the maximum production being detected at 42 h after inoculation, whereas the maximum production of BDSF was observed at 36 h after inoculation. When grown in a rich medium such as YEB, LB, PSA, and NYG, <it>Xoo </it>produced all the three signals with the majority being DSF. Whereas in nutritionally poor XOLN medium <it>Xoo </it>only produced BDSF and DSF but the majority was BDSF.</p> <p>Conclusions</p> <p>This study demonstrates that <it>Xoo </it>and <it>Xcc </it>share the conserved mechanisms for DSF biosynthesis and autoregulation. <it>Xoo </it>produces DSF, BDSF and CDSF signals in rich media and CDSF is a novel signal in DSF-family with two double bonds. All the three DSF-family signals promote EPS production and xylanase activity in <it>Xoo</it>, but CDSF is less active than its analogues DSF and BDSF. The composition and ratio of the three DSF-family signals produced by <it>Xoo </it>are influenced by the composition of culture media.</p

Noise suppression of on-chip mechanical resonators by chaotic coherent feedback

We propose a method to decouple the nanomechanical resonator in optomechanical systems from the environmental noise by introducing a chaotic coherent feedback loop. We find that the chaotic controller in the feedback loop can modulate the dynamics of the controlled optomechanical system and induce a broadband response of the mechanical mode. This broadband response of the mechanical mode will cut off the coupling between the mechanical mode and the environment and thus suppress the environmental noise of the mechanical modes. As an application, we use the protected optomechanical system to act as a quantum memory. It's shown that the noise-decoupled optomechanical quantum memory is efficient for storing information transferred from coherent or squeezed light

Various criteria in the evaluation of biomedical named entity recognition

BACKGROUND: Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated corpora, GENIA and GENETAG, are most frequently used for training and testing biomedical named entity recognition (Bio-NER) systems. JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance. This paper details these differences and describes alternative criteria. We then examine the impact of different criteria and annotation schemes on system performance by retesting systems participated in the above two tasks. RESULTS: To analyze the difference between JNLPBA's and BioCreAtIvE's evaluation, we conduct Experiment 1 to evaluate the top four JNLPBA systems using BioCreAtIvE's classification scheme. We then compare them with the top four BioCreAtIvE systems. Among them, three systems participated in both tasks, and each has an F-score lower on JNLPBA than on BioCreAtIvE. In Experiment 2, we apply hypothesis testing and correlation coefficient to find alternatives to BioCreAtIvE's evaluation scheme. It shows that right-match and left-match criteria have no significant difference with BioCreAtIvE. In Experiment 3, we propose a customized relaxed-match criterion that uses right match and merges JNLPBA's five NE classes into two, which achieves an F-score of 81.5%. In Experiment 4, we evaluate a range of five matching criteria from loose to strict on the top JNLPBA system and examine the percentage of false negatives. Our experiment gives the relative change in precision, recall and F-score as matching criteria are relaxed. CONCLUSION: In many applications, biomedical NEs could have several acceptable tags, which might just differ in their left or right boundaries. However, most corpora annotate only one of them. In our experiment, we found that right match and left match can be appropriate alternatives to JNLPBA and BioCreAtIvE's matching criteria. In addition, our relaxed-match criterion demonstrates that users can define their own relaxed criteria that correspond more realistically to their application requirements

Graphene Field-Effect Transistor for Terahertz Modulation

The real-world applications of terahertz (THz) technology necessitate versatile adaptive optical components, for example, modulators. In this chapter, we begin with a brief review on different techniques for THz modulation. After that, we introduce the extraordinary features of graphene along with its advantages and disadvantages as channel materials for field effect transistor (FET). We then discuss two types of graphene FET-based THz modulators, one is rigid and another is flexible. The feasibility of the high-quality THz modulators with different graphene FET structures has been successfully demonstrated. It is observed that by tuning the carrier concentration of graphene by electrical gating, the THz modulation can be obtained with relatively large modulation depth, broad width band, and moderate speed. This chapter helps the reader in obtaining guidelines for the proper choice of a specific structure for THz modulator with graphene FET

Complications after radical gastrectomy following FOLFOX7 neoadjuvant chemotherapy for gastric cancer

<p>Abstract</p> <p>Background</p> <p>This study assessed the postoperative morbidity and mortality occurring in the first 30 days after radical gastrectomy by comparing gastric cancer patients who did or did not receive the FOLFOX7 regimen of neoadjuvant chemotherapy.</p> <p>Methods</p> <p>We completed a retrospective analysis of 377 patients after their radical gastrectomies were performed in our department between 2005 and 2009. Two groups of patients were studied: the SURG group received surgical treatment immediately after diagnosis; the NACT underwent surgery after 2-6 cycles of neoadjuvant chemotherapy.</p> <p>Results</p> <p>There were 267 patients in the SURG group and 110 patients in the NACT group. The NACT group had more proximal tumours (P = 0.000), more total/proximal gastrectomies (P = 0.000) and longer operative time (P = 0.005) than the SURG group. Morbidity was 10.0% in the NACT patients and 17.2% in the SURG patients (P = 0.075). There were two cases of postoperative death, both in the SURG group (P = 1.000). No changes in complications or mortality rate were observed between the SURG and NACT groups.</p> <p>Conclusion</p> <p>The FOLFOX7 neoadjuvant chemotherapy is not associated with increased postoperative morbidity, indicating that the FOLFOX7 neoadjuvant chemotherapy is a safe choice for the treatment of local advanced gastric cancer.</p

4,4′-Dimethyl-1,1′-[ethyl­enedioxy­bis(nitrilo­methyl­idyne)]dibenzene

The Schiff base, C18H20N2O2, which lies about an inversion centre, adopts a linear conformation. The mol­ecules are packed by C—H⋯π inter­actions, forming a two-dimensional supra­molecular network