Additional file 2 of Chromosome constitution and genetic relationships of Morus spp. revealed by genomic in situ hybridization

Additional file 2: Supplementary Table 1. List of the mulberry accessions used in this study

A Locked Nucleic Acid (LNA)-Based Real-Time PCR Assay for the Rapid Detection of Multiple Bacterial Antibiotic Resistance Genes Directly from Positive Blood Culture

<div><p>Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA)-based quantitative real-time PCR (LNA-qPCR) method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1–10 colony forming units (CFU) per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4%) were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates.</p></div

Analysis of positive blood culture samples by real-time PCR.

<p>Note: the positive blood culture samples containing <i>P</i>. <i>aeruginosa</i> are not included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120464#pone.0120464.t004" target="_blank">Table 4</a>.</p><p>^a: ß-lactamase: <i>bla</i>_CTX-M-1/<i>bla</i>_CTX-M-9 ESBLs or <i>bla</i>_CMY-2/<i>bla</i>_DHA-1 pAmpC gene.</p><p>^b: Eco, <i>Escherichia coli</i>; Kpn, <i>Klebsiella pneumoniae</i>; Pae: <i>Pseudomonas aeruginosa</i>; Sau, <i>Staphylococcus aureus</i>; Sep, <i>S</i>. <i>epidermidis</i>; Sha, <i>S</i>. <i>haemolyticus</i>; Sho, <i>S</i>. <i>hominis</i>, Efm, <i>Enterococcus faecium</i>; Efs, <i>E</i>. <i>faecalis</i>; and Staph, <i>Staphylococcus</i>.</p><p>^c: <i>van</i>A and <i>van</i>B were not detected in the collected cultures.</p><p>Analysis of positive blood culture samples by real-time PCR.</p

Sequences of primers and LNA probes.

<p>^a: The sequence of the LNA probe was completely shown and all the nucleotides in the LNA probe were LNA nucleotides.</p><p>Sequences of primers and LNA probes.</p

Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method

While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling

Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method

While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling

Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method

While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling

Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method

While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling

Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method

While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling

Additional file 1: Table S1. of Distribution patterns of haplotypes for symbionts from Umbilicaria esculenta and U. muehlenbergii reflect the importance of reproductive strategy in shaping population genetic structure

Haplotypes information of Umbilicaria and other six lichen genera across six sites. Table S2. Sequences retrieved from Genbank. Table S3. Primers used in this study. (DOC 285 kb