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Color Plates

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Figures

Image of Color Plate 1 (chapter 21)

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Color Plate 1 (chapter 21)

Directional actin polymerization by isolates were processed for triple-labeling fluorescence microscopy, 5 h after starting the infection of Vero cells. Bacteria (red) were visualized with a polyclonal anti- antibody, actin (green) with phalloidin, and cell nuclei (blue) with DAPI (4′,6′-diamidino-2-phenylindole). Magnification, ×100.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 2 (chapter 21)

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Color Plate 2 (chapter 21)

Schematic representation of the virulence factors. The localization of factors implicated in adhesion (green), entry (blue), escape from the phagosome and intracellular growth (red), and intracytoplasmic movement and cell-to-cell spreading (purple) are indicated. The names of factors whose expression is regulated by PrfA are in orange.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 3 (chapter 31)

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Color Plate 3 (chapter 31)

Acid-fast staining. (A) . (B) . (C) . (Bars, 20 μm.)

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 4 (chapter 42)

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Color Plate 4 (chapter 42)

Genome atlas of NCFM. The atlas represents a circular view of the complete genome sequence of NCFM. The key on the right describes the single circles in the top-down-outermost-innermost direction, as follows. Circle 1 (innermost), GC-skew. Circle 2, COG classification. Predicted open reading frames (ORFs) were analyzed using the COG database and grouped into five major categories: 1, information storage and processing; 2, cellular processes and signaling; 3, metabolism; 4, poorly characterized; 5, ORFs with uncharacterized COGs or no COG assignment. Circle 3, ORF orientation. ORFs in the sense orientation (ORF+) are shown in blue; ORFs in the anti-sense orientation (ORF−) are shown in red. Circle 4, BLAST similarities. Deduced amino acid sequences compared against the nonredundant (nr) database using gapped BLASTP (12). Regions in blue represent unique proteins in NCFM, whereas highly conserved features are shown in red. The degree of color saturation corresponds to the level of similarity. Circle 5, G+C content deviation. Deviations from the average G+C content are shown in either green (low-GC spike) or orange (high-GC spike). A boxfilter was applied to visualize contiguous regions of low or high deviations. Circle 6, ribosomal machinery. tRNAs, rRNAs, and ribosomal proteins are shown as green, cyan, and red lines, respectively. Clusters of proteins are represented as colored boxes to maintain readability. Circle 7, mobile elements. Predicted transposases are shown as light purple dots, and phage-related integrases are shown as orange dots. Circle 8, stress response. Genes involved in the general stress response, including chaperones, and genes involved in heat shock, DNA repair, and pH regulation are shown as dark purple dots. Circle 9, peptide and amino acid utilization. Proteases and peptidases are shown as green dots, and non-sugar-related transporters are shown as light blue dots. Circle 10 (outermost), two-component regulators (2CRS). Each 2CRS is represented as a brown dot, consisting of a response regulator and a histidine kinase. In circles 7 to 10 each full dot represents one predicted ORF and stacked dots represent clusters of ORFs. Selected features representing single ORFs and ORF clusters are shown outside of circle 10 with bars indicating their absolute size. The origin and terminus of DNA replication are identified in green and red, respectively. Other features: SlpA and SlpB (S-layer proteins), CdpA (cell division protein [50]), sugar utilization (sucrose, fructo-oligosaccharide, trehalose, and raffinose), LacE (phosphotransferase system [PTS]-sugar transporter), BshA and BshB (bile salt hydrolases), Mub-909 to Mub-1709 (mucus-binding proteins; the numbers correspond to the La numbering scheme), FbpA (fibronectin-binding protein), Cfa (cyclopropane fatty acid synthase), Fibronectin_binding (fibronectin-binding protein cluster), EPS_cluster (exopolysaccharides), Lactacin_B (bacteriocin), pauLA-I to pauLA-III (potential autonomous units), and prLA-I and prLA-II (phage remnants). Reprinted from reference 3.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 5 (chapter 44)

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Color Plate 5 (chapter 44)

Genome atlas of WCFS1. The predicted origin of replication is shown at the top. The outer to inner circles show (i) positive-strand ORFs (red); (ii) negative-strand ORFs (blue); (iii) GC-skew (green); (iv) G+C content (black); (v) prophage-related functions (green) and -like elements (purple); and (vi) rDNA operons (black) and tRNA-encoding genes (red). Reprinted from reference 38 with permission.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 6 (chapter 44)

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Color Plate 6 (chapter 44)

Comparison of the region containing the “virulence gene cluster” of and the homologous region of the and genomes. Open blue boxes and arrows indicate orthologs among the three genomes; solid red boxes and arrows indicate the virulence gene cluster; solid yellow boxes and arrows indicate genes absent from . (A) Scheme generated by GenomeScout (LION Bioscience). (B) Enlargement of the region containing the virulence gene cluster. Reprinted from reference 31 with permission.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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Image of Color Plate 7 (chapter 44)

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Color Plate 7 (chapter 44)

Microarrays. Probes are PCR amplified from clones in a library or from genomic DNA by using gene-specific primers. Individual amplicons are purified and spotted onto glass slides. Total RNA is labeled from both a test and reference sample by using fluorescent dyes and allowed to hybridize to the probes on the array. The array is then visualized using a laser scanner that generates color images, which are overlaid and compared for intensity and source. Adapted from reference 26 with permission.

Citation: Doyle M, Beuchat L. 2007. Color Plates, In Food Microbiology: Fundamentals and Frontiers, Third Edition. ASM Press, Washington, DC.
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