Flow chart of selection process for eligible studies.

<p>Flow chart of selection process for eligible studies.</p

Cloning and Analysis of a Large Plasmid pBMB165 from <i>Bacillus thuringiensis</i> Revealed a Novel Plasmid Organization

<div><p>In this study, we report a rapid cloning strategy for large native plasmids via a contig linkage map by BAC libraries. Using this method, we cloned a large plasmid pBMB165 from <i>Bacillus thuringiensis</i> serovar <i>tenebrionis</i> strain YBT-1765. Complete sequencing showed that pBMB165 is 77,627 bp long with a GC-content of 35.36%, and contains 103 open reading frames (ORFs). Sequence analysis and comparison reveals that pBMB165 represents a novel plasmid organization: it mainly consists of a pXO2-like replicon and mobile genetic elements (an inducible prophage BMBTP3 and a set of transposable elements). This is the first description of this plasmid organization pattern, which may result from recombination events among the plasmid replicon, prophage and transposable elements. This plasmid organization reveals that the prophage BMBTP3 may use the plasmid replicon to maintain its genetic stability. Our results provide a new approach to understanding co-evolution between bacterial plasmids and bacteriophage.</p> </div

Characteristics of the studies included in the meta-analysis.

<p>TP, true positive; FP, false positive; FN, false negative; TN, true negative; CSF, cerebrospinal fluid; PCR, polymerase chain reaction; FQ-PCR, fluorescent quantitative polymerase chain reaction; RT-qPCR, reverse transcription-quantitative PCR; CP, Crossing Point; C_T, cycle threshold; bp, base pairs; NR, no report.</p><p>Characteristics of the studies included in the meta-analysis.</p

Additional file 1 of DNMT3A mutation promotes leukemia development through NAM-NAD metabolic reprogramming

Additional file 1: Table S1. Primer sequences used in Q-RT-PCR

Additional file 2 of DNMT3A mutation promotes leukemia development through NAM-NAD metabolic reprogramming

Additional file 2: Table S2. The mRNA expression level of NAMPT in AML obtained from the Oncomine database

Circular representation of plasmid pBMB165 and graphical representation of the annotation and the structure of the prophage BMBTP3.

<p>The inner circle represents the GC bias [(G - C)/(G + C)], with positive and negative values in reddish brown and cobalt blue, respectively; the second circle represents the GC-content, with positive and negative values in grey and black, respectively; and the outer circle represents the predicted genes on the reverse and forward arrows. The pXO2-like replicon is highlighted with a green arching frame. Regions of transposon and prophage BMBTP3 are annotated beside the corresponding arrows and separated by straight lines. The main functional genes of BMBTP3 are annotated above the extended corresponding arrows at the bottom. Different structural and functional regions are annotated and separated by vertical lines. Color coding for the genes is as follows: olive green, plasmid replication; deep green, prophage replication; deep yellow, plasmid stabilization system; orange, regulatory; red, a predicted camelysin; blue, mobile DNA; purple, phage related; grey, hypothetical protein. The outer scale is marked in kilobases. </p

Summary receiver operating characteristic curve of 16S rRNA gene PCR diagnostic value in bloodstream infections.

<p>Summary receiver operating characteristic curve of 16S rRNA gene PCR diagnostic value in bloodstream infections.</p

Diagnostic Odds Ratio with Cochran-Q value.

<p>Diagnostic Odds Ratio with Cochran-Q value.</p

Forest plots for the diagnostic accuracy of 16S rRNA gene PCR.

<p>A. Sensitivity; B. Specificity; C. Positive likelihood ratio; D. Negative likelihood ratio.</p

Comparison of pBMB165 and homologous plasmids and phages by Easyfig alignment.

<p>Coding Sequences (CDSs) are represented by colored arrows. Predicted functions/homologies are indicated by the color key featured below. The pXO2-like replicon is highlighted with a green frame. Color coding for the genes is as follows: olive green, plasmid replication; deep green, prophage replication; deep yellow, plasmid stabilization system; orange, regulatory; red, a predicted camelysin; blue, mobile DNA; purple, phage related; grey, hypothetical protein; midnight blue, conjugation-related proteins; wine, capsule synthesis related proteins; and brown, other determinants. Highly conserved segments of the plasmids and phages are paired by shaded regions, with the darker shading reflecting a greater amino acid identity, from 66% (A) or 63% (B) to 100%. The regions outside the shaded regions lack homology between plasmids and phages. The outer scale is marked in kilobases.</p