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PMC:PMC3652863 JSONTXT

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div. section text # proj. length # Ann.
0 TIAB Genomic and Proteomic Analyses of the Terminally Redundant Genome of thePseudomonas aeruginosaPhage 1 1576 0 show
1 Introduction Bacteriophages (phages) are ubiquitous in the biosphere [1]. Estimations of phage numbers, ranging f 1 3563 0 show
2 Results Morphology of PaP1 PaP1 is in structure and dimensions identical to P. aeruginosa phage PB1 [14]. Th 1 735 0 show
3 Results Biological characteristics of PaP1 PaP1 forms clear plaques (∼3 mm in diameter) surrounded by a smal 1 699 0 show
4 Results General genomic characteristics of PaP1 The genome of PaP1 consists of 91,715 base pairs (bp) with a 1 1034 0 show
5 Results Determination of PaP1 genome termini The PaP1 genome was assembled as a circular molecule when seque 1 1594 0 show
6 Results Identification and organization of PaP1 genes The open reading frames (ORFs) of the PaP1 genome were 1 3180 0 show
7 Results Identification of phage PaP1 structural proteins A dsDNA phage particle is made up of a series of st 1 2443 0 show
8 Results Comparative genomic analysis of PaP1, JG004, PAK_P1, and vB_PaeM_C2-10_Ab1 Comparative analysis of g 1 3777 0 show
9 Discussion In the present work, the newly isolated phage PaP1 was assigned as a member of the Myoviridae family 1 4146 0 show
10 Materials and Methods Pseudomonas aeruginosa strains Six P. aeruginosa strains (PA1, PA2, PA3, PA4, PA5, and PA6) were iso 1 465 0 show
11 Materials and Methods Phage propagation and purification Phage PaP1 was isolated from the hospital sewage using P. aerugin 1 1263 0 show
12 Materials and Methods Transmission electron microscopy (TEM) Filtered phage lysates (about 1011 PFU/mL) were sedimented fo 1 618 0 show
13 Materials and Methods DNA extraction and sequencing EDTA to a final concentration of 20 mM, proteinase K at 50 µg mL−1, an 1 1030 0 show
14 Materials and Methods Analysis of PaP1 genome ends Simulation of the restriction enzyme mapping of the PaP1 genome sequenc 1 2015 0 show
15 Materials and Methods Sequence analysis and genome annotation The software packages DNAStar [46] and DNAMAN (http://www.ly 1 811 0 show
16 Materials and Methods SDS-PAGE and HPLC-MS of the PaP1 structural proteins The purified phage particles were resuspended i 1 952 0 show
17 Materials and Methods Comparative genome analysis Sequences of the P. aeruginosa phages JG004 [31], vB_PaeM_C2-10_Ab1 (Gen 1 793 0 show
18 Caption-Figure 1 Electron micrographs of purified PaP1 phage particles. A shows two PaP1 particles with uncontracted 1 403 0 show
19 Caption-Figure 2 One-step growth curve of phage PaP1. Experiments were repeated three times with duplicate samples. T 1 172 0 show
20 Caption-Figure 3 Circular conformation of GC skew and GC plot of the PaP1 genome. The GC skew is calculated as (G-C)/ 1 402 0 show
21 Caption-Figure 4 Identification of PaP1 genome ends. (A) Digestion of the PaP1 genome DNA by NarI and NotI. The red a 1 1354 0 show
22 Caption-Figure 5 Structure of PaP1 terminal redundancy. (A) PaP1 genome DNA with terminal redundancy at both ends. Th 1 388 0 show
23 Caption-Figure 6 Diagram of the PaP1 genome with functional annotations. Blue arrowheads show genes on the plus stran 1 344 0 show
24 Caption-Figure 7 SDS-PAGE analysis of the structural proteins of phage PaP1. Proteins were visualized in a 15% (w/v) 1 149 0 show
25 Caption-Figure 8 Pairwise nucleotide sequence comparison of phages closely related to PaP1. Comparisons were conducte 1 395 0 show
26 Caption-Figure 9 Dot plot of genome sequences of six phages using the program Gepard. The word length used is 9 bp; o 1 298 0 show
27 Caption-Figure 10 Phylogenetic analysis of major capsid protein amino acid sequences. The diagram was constructed usin 1 487 0 show
28 Caption-Table 1 General features of the PaP1 genome. 1 36 0 show
29 Caption-Table 2 Predicted promoters of the PaP1 genome. 1 39 0 show
30 Caption-Table 3 Putative terminators of the PaP1 genome. 1 40 0 show
31 Caption-Table 4 Mass spectrometry identification of PaP1 structural proteins. 1 61 0 show
32 Caption-Table 5 Comparison of phages with BlastN scores of more than 200 against the PaP1 genome. 1 81 0 show
33 Caption-Table 6 Overview of genomic characteristics of Myoviridae that infect P. aeruginosa. 1 76 0 show