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PMC:1913099 JSONTXT

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div. section text # proj. length # Ann.
0 TIAB Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes Bacteria–host i 2 1716 2 show
1 Introduction Microarray technology is now commonly used to reveal genome-wide transcriptional changes in bacteria 2 4792 8 show
2 Results/Discussion Adherence-Mediated Differential Expression We developed spotted oligonucleotide arrays of the S. pyo 2 1502 4 show
3 Results/Discussion Verification by Quantitative Real-Time PCR We conducted TaqMan (qRT-PCR) analysis [23] of 11 differe 2 987 0 show
4 Results/Discussion Virulence Factors Streptococci elaborate several factors implicated in infection, including surface- 2 3174 36 show
5 Results/Discussion Phage-Encoded Genes SF370 contains one inducible prophage (370.1) and three defective prophages (370 2 606 4 show
6 Results/Discussion Allelic Replacement of speH Increased expression of speH during pharyngeal cell adherence suggests t 2 984 12 show
7 Results/Discussion Differential Expression of Genes from Diverse Functional Categories We identified a number of genes 2 1702 18 show
8 Results/Discussion Neighbor Clustering Our initial analysis revealed the differential expression of a wide range of fun 2 5139 1 show
9 Results/Discussion Type I Clusters: Intact Metabolic Pathways and Multimeric Proteins We measured the performance of ou 2 4606 45 show
10 Results/Discussion Type II Clusters Based on the Type I cluster results, we speculated that genes contained in Type II 2 3777 33 show
11 Results/Discussion Allelic Replacement of spy0129 We created a spy0129 deletion mutant in strain SF370 (SF370Δspy0129) 2 2071 25 show
12 Results/Discussion Additional Type II Cluster Example Another cluster, spy1725–1719, contained six genes that together 2 1347 22 show
13 Results/Discussion Neighbor Clustering and Operons Although neighbor clustering is not an operon-predicting method, we 2 838 4 show
14 Results/Discussion Analysis of Previously Published Array Data We applied the statistical analysis and the GenomeCrawle 2 3741 30 show
15 Results/Discussion Concluding Remarks Although GenomeCrawler improves bacterial array analyses, it has limitations: it 2 2733 3 show
16 Methods Spotted oligonucleotide microarrays. Sense strand oligonucleotides (primarily 55-mers), representing 2 676 0 show
17 Methods Bacterial cultures. For adherence assays, S. pyogenes strain SF370 (kindly provided by J. Ferretti, 2 778 0 show
18 Methods Pharyngeal cell association and adherence assay. Assays on streptococcal adherence to human pharynge 2 954 0 show
19 Methods RNA isolation. Recovered streptococci were washed twice in PBS and lysed with the amidase enzyme lys 2 580 0 show
20 Methods Synthesis of cDNA and labeling. DNase-treated streptococcal RNA (5 μg) was reverse-transcribed using 2 657 0 show
21 Methods Microarray hybridization and image acquisition. Four biological replicate experiments incorporating 2 700 0 show
22 Methods Data filtering, normalization, statistical significance analysis, and calculation of PF values for i 2 2076 0 show
23 Methods Real-time qRT-PCR primers, probes, and plasmid standards. We performed real-time qRT-PCR analysis (T 2 1116 0 show
24 Methods Real-time qRT-PCR and TaqMan analysis. We used a two-step RT-PCR procedure to reverse transcribe RNA 2 1968 0 show
25 Methods RT-PCR of spy0127–0130 cluster. The sequences of forward (F) and reverse (R) primers for each of the 2 1094 0 show
26 Methods Allelic replacement of the speH and spy0129 genes in SF370. The strategy for allelic replacement of 2 1356 0 show
27 Methods Biological assay: Pharyngeal cell adherence. We tested late-logarithmic phase SF370ΔspeH and SF370Δs 2 387 0 show
28 Methods Neighbor clustering. We provide a general explanation of the principles of neighbor clustering follo 2 2597 0 show
29 Methods Theoretical basis for GenomeCrawler. Conceptually, PF reflects the physical change in gene expressio 2 1463 0 show
30 Methods GenomeCrawler algorithms and calculation of p-values. PE ( , tg, K), called the expression P-va 2 2500 0 show
31 Methods Relationship between PF and PC. We define the relationship between PF ( ) and PC (tg | K), as b 2 1279 0 show
32 Methods Identification of putative operons. The published SF370 genome does not contain promoter annotations 2 648 0 show
33 Methods Analysis of previously published streptococcal microarray data. We analyzed recently published micro 2 519 0 show
34 Methods Software and microarray datasets. For MIAME (Minimum Information About a Microarray Experiment) comp 2 521 0 show
35 Caption-Figure 1 Confirmation of speH Deletion Mutant and Pharyngeal Cell Adherence Assay (A) Results of RT-PCR and P 2 1163 0 show
36 Caption-Figure 2 Statistically Significant Neighbor Clusters in the SF370 Genome Neighbor clusters that adhere to the 2 1736 0 show
37 Caption-Figure 3 Neighbor Cluster spy0127–0130 (A) Schematic representation of the spy0127–0130 cluster. Gene size (b 2 880 0 show
38 Caption-Figure 4 Confirmation of spy0129 Deletion Mutant and Adherence Assay Top panel is a schematic representation 2 1342 0 show
39 Caption-Table 1 Summary of Streptococcal Genes Exhibiting Significant Changes in Expression during Adherence to Phar 2 159 0 show
40 Caption-Table 2 Functional Categories of Streptococcal Genes Exhibiting Significant Changes in Expression during Adh 2 173 0 show
41 Caption-Table 3 Qualifying Neighbor Clusters Identified in the S. pyogenes SF370 Genome by GenomeCrawler Analysis of 2 143 0 show