Schematic representation of multiple drug-resistance determinants.

<p>Pairwise comparison of plasmid regions around the <i>bla</i>_NDM-1 gene in pNDM-1_Dok01, pNDM-HK, and pKpANDM-1 in <i>K. pneumoniae</i> KP-05-506 and <i>E. coli</i> strain 271 by a BLASTN homology search and visualized with the ACT program. The <i>bla</i>_NDM-1 genes are identical among the aligned sequences. The red and blue bars between the DNA represent individual nucleotide matches in the forward and inverted directions, respectively. BLASTN match scores of <300 are not shown.</p

Phylogenetic tree of the whole amino acid sequences of chaperonin GroES homologs.

<p>Detailed analysis is same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025334#pone-0025334-g003" target="_blank">Fig. 3</a>.</p

Circular representation of the <i>E. coli</i> NDM-1_Dok01 plasmid pNDM-1_Dok01.

<p>From the outside inwards, the outer circle indicates the homologous regions to the <i>E. coli</i> strain AR060302 plasmid pAR060302 (red) and <i>E. coli</i> strain HK-01 plasmid pNDM-HK (orange). The second circle shows the size in base pairs (bp). The third and fourth circles show the positions of the CDSs transcribed in the clockwise and anti-clockwise directions, respectively (using color codes according to the clusters of orthologous groups (COG) classification table and additional customized categories). The fifth circle shows a plot of the G + C content (in 0.5 kb windows).</p

Phylogenetic tree of the whole amino acid sequences of chaperonin GroEL homologs.

<p>The amino acid sequences were selected and retrieved with a BLASTP search against the refseq_protein database with a cut-off value of 75% identity. The tree was constructed using the maximum likelihood method with 1,000 bootstrap replicates. The scale indicates that a branch length of 0.03 is 3 times as long as one that would show a 1% difference between the amino acid sequences at the beginning and end of the branch. The number at each branch node represents the bootstrapping value. The chromosomal GroEL in <i>E. coli</i> NDM-1_Dok01 is highlighted in blue. The GC percentage of the respective nucleotide sequences is shown on the right-hand side of the figure.</p

ORFs in NDM-1 composite transposon.

<p>ORFs in NDM-1 composite transposon.</p

Mitochondrial genome maps of <i>Kudoa</i> species.

<p>Outer circle: protein-coding genes are represented by blue arrows, rRNAs by gray arrows and tRNAs by green arrowheads. Middle circle: plot of AT skew with the positive value towards the outside. Inner circle: plot of GC-content with higher %GC towards the outside.</p

Genetic Variation of Human Papillomavirus Type 16 in Individual Clinical Specimens Revealed by Deep Sequencing

<div><p>Viral genetic diversity within infected cells or tissues, called viral quasispecies, has been mostly studied for RNA viruses, but has also been described among DNA viruses, including human papillomavirus type 16 (HPV16) present in cervical precancerous lesions. However, the extent of HPV genetic variation in cervical specimens, and its involvement in HPV-induced carcinogenesis, remains unclear. Here, we employ deep sequencing to comprehensively analyze genetic variation in the HPV16 genome isolated from individual clinical specimens. Through overlapping full-circle PCR, approximately 8-kb DNA fragments covering the whole HPV16 genome were amplified from HPV16-positive cervical exfoliated cells collected from patients with either low-grade squamous intraepithelial lesion (LSIL) or invasive cervical cancer (ICC). Deep sequencing of the amplified HPV16 DNA enabled <i>de novo</i> assembly of the full-length HPV16 genome sequence for each of 7 specimens (5 LSIL and 2 ICC samples). Subsequent alignment of read sequences to the assembled HPV16 sequence revealed that 2 LSILs and 1 ICC contained nucleotide variations within E6, E1 and the non-coding region between E5 and L2 with mutation frequencies of 0.60% to 5.42%. In transient replication assays, a novel E1 mutant found in ICC, E1 Q381E, showed reduced ability to support HPV16 origin-dependent replication. In addition, partially deleted E2 genes were detected in 1 LSIL sample in a mixed state with the intact E2 gene. Thus, the methods used in this study provide a fundamental framework for investigating the influence of HPV somatic genetic variation on cervical carcinogenesis. </p> </div

The phylogenetic tree of mitochondrial-encoded proteins.

<p>The trees were inferred using the maximum-likelihood method and bootstrapped 100 times. Branches with bootstrap support ≥80% are colored black, and those with support <80% are colored gray with the support value denoted.</p

The relative rates of nonsynonymous and synonymous substitutions in mitochondrial-encoded protein genes, compared among the genus <i>Kudoa</i> and other cnidarian classes.

<p>The relative rates of nonsynonymous and synonymous substitutions in mitochondrial-encoded protein genes, compared among the genus <i>Kudoa</i> and other cnidarian classes.</p

Mutation frequency profile of full-length HPV16 genomes in W12 cells.

<p>The read sequences obtained with full-length HPV16 genomes prepared from W12 cells were aligned to the reference HPV16 sequence (AF125673), and mutation/error frequencies at each nucleotide position are presented in the landscape of the full-length HPV16 genome. A threshold line for a reliable mutation frequency (0.5%) is indicated with the red dotted line. The genome organization of HPV16 is indicated above.</p