Color Plates
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Editors:
Fabiano L. Thompson,
Brian Austin,
Jean Swings
Content Type: Monograph
Source:
The Biology of Vibrios
Publication Year:
2006
Category: Environmental Microbiology
e-ISBN
:
9781555815714
Book DOI:
10.1128/9781555815714
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Figures
Color Plates
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch02cp01
Color Plate 1 (Chapter 2)
Colonial morphology of vibrios in different media. (a) Estuarine water plated on marine agar. (b) Estuarine water plated on TCBS agar after 24 h of incubation. (c) Vibrios on TCBS agar; note non-vibrios forming very small colonies (arrows). (d) V. alginolyticus on marine agar. (e) V. alginolyticus on TSA agar; note spreading on this medium. (f) V. alginolyticus on TCBS agar, a sucrose-positive colony. (g) V. parahaemolyticus on TCBS agar, a sucrose-negative colony. (h) V. parahaemolyticus on CHROMagar chromogenic agar; note the violet color of the colonies. (i) Cryopreservation glass bead (arrow) streaked onto TSA.
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Color Plate 1 (Chapter 2)
Colonial morphology of vibrios in different media. (a) Estuarine water plated on marine agar. (b) Estuarine water plated on TCBS agar after 24 h of incubation. (c) Vibrios on TCBS agar; note non-vibrios forming very small colonies (arrows). (d) V. alginolyticus on marine agar. (e) V. alginolyticus on TSA agar; note spreading on this medium. (f) V. alginolyticus on TCBS agar, a sucrose-positive colony. (g) V. parahaemolyticus on TCBS agar, a sucrose-negative colony. (h) V. parahaemolyticus on CHROMagar chromogenic agar; note the violet color of the colonies. (i) Cryopreservation glass bead (arrow) streaked onto TSA.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch05cp02
Color Plate 2 (Chapter 5)
Comparison of relative positions of conserved genes among Vibrio and Photobacterium species. Gene pairs were generated by BLASTp analysis of predicted genes from each genome. Lines connect conserved genes among the organisms. The chromosomes are depicted with the origins of replication at the left end. VC, V. cholerae (Heidelberg et al., 2000); VV, V. vulnificus (Chen et al., 2003); VP, V. parahaemolyticus (Makino et al., 2003); PP, P. profundum (GenBank accession nos. CR354531 and CR354532).
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Color Plate 2 (Chapter 5)
Comparison of relative positions of conserved genes among Vibrio and Photobacterium species. Gene pairs were generated by BLASTp analysis of predicted genes from each genome. Lines connect conserved genes among the organisms. The chromosomes are depicted with the origins of replication at the left end. VC, V. cholerae (Heidelberg et al., 2000); VV, V. vulnificus (Chen et al., 2003); VP, V. parahaemolyticus (Makino et al., 2003); PP, P. profundum (GenBank accession nos. CR354531 and CR354532).
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch06cp03
Color Plate 3 (Chapter 6)
The functional landscape of the paranome. Preferentially retained duplicated genes according to their functional classes are visualized for all Vibrionaceae genomes. The functional distribution of the paranome in terms of percentages is subtracted from the functional distribution of the single-copy genes in terms of percentages, revealing the functional classes that have relatively more (yellow to red) or less (gradient of blue) paralogs compared to single-copy genes. The functional classes have been ordered according to relative average contribution. The paranome was divided into the fraction that is not in duplicated segments (A) and the fraction that is in duplicated segments (B). The different functional classes are abbreviated as follows: [C] energy production and conversion, [D] cell cycle control, cell division, chromosome partitioning, [E] amino acid transport and metabolism, [F] nucleotide transport and metabolism, [G] carbohydrate transport and metabolism, [H] coenzyme transport and metabolism, [I] lipid transport and metabolism, [J] translation, ribosomal structure, and biogenesis, [K] transcription, [L] replication, recombination, and repair, [M] cell wall/membrane/envelope biogenesis, [N] cell motility, [O] posttranslational modification, protein turnover, chaperones, [P] inorganic ion transport and metabolism, [Q] secondary metabolite biosynthesis, transport, and catabolism, [R] general function prediction only, [S] function unknown, [U] intracellular trafficking, secretion, and vesicular transport, [V] defense mechanisms, [X] none of the above. Note that all genes or open reading frames annotated as being transposon or phage related have been removed from this analysis.
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Color Plate 3 (Chapter 6)
The functional landscape of the paranome. Preferentially retained duplicated genes according to their functional classes are visualized for all Vibrionaceae genomes. The functional distribution of the paranome in terms of percentages is subtracted from the functional distribution of the single-copy genes in terms of percentages, revealing the functional classes that have relatively more (yellow to red) or less (gradient of blue) paralogs compared to single-copy genes. The functional classes have been ordered according to relative average contribution. The paranome was divided into the fraction that is not in duplicated segments (A) and the fraction that is in duplicated segments (B). The different functional classes are abbreviated as follows: [C] energy production and conversion, [D] cell cycle control, cell division, chromosome partitioning, [E] amino acid transport and metabolism, [F] nucleotide transport and metabolism, [G] carbohydrate transport and metabolism, [H] coenzyme transport and metabolism, [I] lipid transport and metabolism, [J] translation, ribosomal structure, and biogenesis, [K] transcription, [L] replication, recombination, and repair, [M] cell wall/membrane/envelope biogenesis, [N] cell motility, [O] posttranslational modification, protein turnover, chaperones, [P] inorganic ion transport and metabolism, [Q] secondary metabolite biosynthesis, transport, and catabolism, [R] general function prediction only, [S] function unknown, [U] intracellular trafficking, secretion, and vesicular transport, [V] defense mechanisms, [X] none of the above. Note that all genes or open reading frames annotated as being transposon or phage related have been removed from this analysis.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch06cp04
Color Plate 4 (Chapter 6)
Visualization of segmental duplication and conservation among Vibrionaceae. (Top) Segmental duplication in a genomic fragment of the V. vulnificus CMCP6 chromosome I (gene 900 to 1050). Each block is a segmental duplication where the width represents the number of genes in the segment, and the height is the number of homologous copies found in the genome. (Bottom) Colinearity between the V. vulnificus CMCP6 genomic fragment and other Vibrionaceae. Conservation of gene content and order is represented by the colored lines. Conservation of content without order is represented by gray lines. When a colinear region is also duplicated in segments, a red line is drawn. The scale in the ruler is 10 genes between two lines. Blocks labeled with 1 and 3 are homologous segments unique in V. vulnificus CMCP6, whereas blocks 2 and 4 are conserved in all Vibrionaceae.
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Color Plate 4 (Chapter 6)
Visualization of segmental duplication and conservation among Vibrionaceae. (Top) Segmental duplication in a genomic fragment of the V. vulnificus CMCP6 chromosome I (gene 900 to 1050). Each block is a segmental duplication where the width represents the number of genes in the segment, and the height is the number of homologous copies found in the genome. (Bottom) Colinearity between the V. vulnificus CMCP6 genomic fragment and other Vibrionaceae. Conservation of gene content and order is represented by the colored lines. Conservation of content without order is represented by gray lines. When a colinear region is also duplicated in segments, a red line is drawn. The scale in the ruler is 10 genes between two lines. Blocks labeled with 1 and 3 are homologous segments unique in V. vulnificus CMCP6, whereas blocks 2 and 4 are conserved in all Vibrionaceae.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch08cp05
Color Plate 5 (Chapter 8)
Comparison of relative positions of conserved ORFs between V. vulnificus YJ016 and CMCP6 superintegron regions. ORF pairs were generated by BLASTn analysis of predicted genes from each genome. Pairs with a BLASTp score ≥600 are shown. Red lines connect both conserved genes between the two organisms. Cassette-encoded ORFs are symbolized by blue boxes, the intIA gene is shown as a red box, and white boxes correspond to ORFs located outside the SI; the relative orientation of the ORFs is also shown.
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Color Plate 5 (Chapter 8)
Comparison of relative positions of conserved ORFs between V. vulnificus YJ016 and CMCP6 superintegron regions. ORF pairs were generated by BLASTn analysis of predicted genes from each genome. Pairs with a BLASTp score ≥600 are shown. Red lines connect both conserved genes between the two organisms. Cassette-encoded ORFs are symbolized by blue boxes, the intIA gene is shown as a red box, and white boxes correspond to ORFs located outside the SI; the relative orientation of the ORFs is also shown.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch14cp06
Color Plate 6 (Chapter 14)
Light organs of Euprymna scolopes juveniles. (A) A juvenile placed ventral side up and lit from above. Red box indicates location of light organ. Gold color within light organ is reflective tissue. (B) Backlit light organ. Translucent symbiotic tissue sits above the darker ink sac. (C) Similar to panel B, except epifluorescence microscopy reveals the location of green fluorescent protein-labeled V. fischeri (green) within the light organ. (D) Transmission electron microscopy of bacterial symbionts (green) colonizing microvillous surface (mv) of a crypt epithelial cell (ep). (E) Scanning electron microscopy of a light organ colored to show ciliated fields on the light organ surface (yellow) and other light organ tissues (blue). The white arrow indicates the approximate location of three 10- to 15-μm-diameter pores. (F) Cartoon depiction of a light organ, with yellow and blue coloration as in panel E. White regions indicate integral internal symbiotic tissues, described in the text, with numbers labeling crypts 1, 2, and 3, respectively. Solid bars in panels A, B, C, and E are ~250 μm.
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Click to view
Color Plate 6 (Chapter 14)
Light organs of Euprymna scolopes juveniles. (A) A juvenile placed ventral side up and lit from above. Red box indicates location of light organ. Gold color within light organ is reflective tissue. (B) Backlit light organ. Translucent symbiotic tissue sits above the darker ink sac. (C) Similar to panel B, except epifluorescence microscopy reveals the location of green fluorescent protein-labeled V. fischeri (green) within the light organ. (D) Transmission electron microscopy of bacterial symbionts (green) colonizing microvillous surface (mv) of a crypt epithelial cell (ep). (E) Scanning electron microscopy of a light organ colored to show ciliated fields on the light organ surface (yellow) and other light organ tissues (blue). The white arrow indicates the approximate location of three 10- to 15-μm-diameter pores. (F) Cartoon depiction of a light organ, with yellow and blue coloration as in panel E. White regions indicate integral internal symbiotic tissues, described in the text, with numbers labeling crypts 1, 2, and 3, respectively. Solid bars in panels A, B, C, and E are ~250 μm.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch16cp07
Color Plate 7 (Chapter 16)
A colony of O. patagonica showing bleached and healthy tissues.
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Click to view
Color Plate 7 (Chapter 16)
A colony of O. patagonica showing bleached and healthy tissues.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch16cp08
Color Plate 8 (Chapter 16)
Photograph of the fireworm H. carunculata feeding on a coral colony.
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Click to view
Color Plate 8 (Chapter 16)
Photograph of the fireworm H. carunculata feeding on a coral colony.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch16cp09
Color Plate 9 (Chapter 16)
Photographs of a bacterium-bleached P. damicornis coral (a) and a healthy one (b).
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Click to view
Color Plate 9 (Chapter 16)
Photographs of a bacterium-bleached P. damicornis coral (a) and a healthy one (b).
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch17cp10
Color Plate 10 (Chapter 17)
The two historical entrance routes of cholera to South America (heavy arrows). Major dissemination route of cholera in Brazil in the 1991 pandemic (light arrows). Foci of distinct nonepidemic V. cholerae lineages in the South American pandemic (1991): purple, Tucumán strain; orange, Amazonia strain; and blue, sucrose late-fermenting strain.
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Color Plate 10 (Chapter 17)
The two historical entrance routes of cholera to South America (heavy arrows). Major dissemination route of cholera in Brazil in the 1991 pandemic (light arrows). Foci of distinct nonepidemic V. cholerae lineages in the South American pandemic (1991): purple, Tucumán strain; orange, Amazonia strain; and blue, sucrose late-fermenting strain.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch17cp11
Color Plate 11 (Chapter 17)
Comparison of the proteins present in supernatant-enriched fractions of the Amazonia strain 3509 and the El Tor strain N16961, in the pH range of 4 to 7 (left to right), and M
r from 10 to 110 kDa. The 2D gels were stained with Coomassie blue. (A) 2D gels for each strain. The seven pairs of orange spots in this panel correspond to proteins with the same identification and position in both gels. They were used as reference spots for the alignment of the rest of the gels. (B) The same gels with superimposed orange spots for the identified proteins. The numbers correspond to those in Table 1. Spots were numbered from left to right and from top to bottom. Proteins with the same identification received the same number in both gels.
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Click to view
Color Plate 11 (Chapter 17)
Comparison of the proteins present in supernatant-enriched fractions of the Amazonia strain 3509 and the El Tor strain N16961, in the pH range of 4 to 7 (left to right), and M r from 10 to 110 kDa. The 2D gels were stained with Coomassie blue. (A) 2D gels for each strain. The seven pairs of orange spots in this panel correspond to proteins with the same identification and position in both gels. They were used as reference spots for the alignment of the rest of the gels. (B) The same gels with superimposed orange spots for the identified proteins. The numbers correspond to those in Table 1. Spots were numbered from left to right and from top to bottom. Proteins with the same identification received the same number in both gels.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch18cp12
Color Plate 12 (Chapter 18)
Genetic organization of pJM1. The colored arrows identify predicted ORFs and their direction of transcription. Red, ORFs related to siderophore biosynthesis; blue, ORFs related to siderophore transport; green, ORFs related to insertion elements and composite transposon; cyan, ORFs related to replication and partitioning; yellow, conserved hypothetical ORFs and ORFs with no known functions; black, ORFs with functions that do not fall in any of the above categories. The black arrowheads represent genes encoding antisense RNAs: rnaA, antisense RNAα, and rnaB, antisense RNAβ.
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Click to view
Color Plate 12 (Chapter 18)
Genetic organization of pJM1. The colored arrows identify predicted ORFs and their direction of transcription. Red, ORFs related to siderophore biosynthesis; blue, ORFs related to siderophore transport; green, ORFs related to insertion elements and composite transposon; cyan, ORFs related to replication and partitioning; yellow, conserved hypothetical ORFs and ORFs with no known functions; black, ORFs with functions that do not fall in any of the above categories. The black arrowheads represent genes encoding antisense RNAs: rnaA, antisense RNAα, and rnaB, antisense RNAβ.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch19cp13
Color Plate 13 (Chapter 19)
Bioluminescent V. harveyi ISO7 isolated from seawater by Phillip Burza. Photograph by Dr. Jane Oakey, James Cook University.
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Color Plate 13 (Chapter 19)
Bioluminescent V. harveyi ISO7 isolated from seawater by Phillip Burza. Photograph by Dr. Jane Oakey, James Cook University.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch19cp14
Color Plate 14 (Chapter 19)
Septic hepatopancreatic tubules from broodstock of P. monodon naturally infected with V. harveyi from northern Australia. Photograph by Leigh Owens.
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Color Plate 14 (Chapter 19)
Septic hepatopancreatic tubules from broodstock of P. monodon naturally infected with V. harveyi from northern Australia. Photograph by Leigh Owens.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch23cp15
Color Plate 15 (Chapter 23)
(A) Micrograph of V. cholerae colonizing the suckling mouse intestine. First image shows villous architecture within the small intestine; inset is a magnification of crypts within the first image detailing V. cholerae cells in intimate contact with epithelial cells. Image courtesy of M. Neal Guentzel. (B) Biofilm structures of green fluorescent protein-expressing V. cholerae as imaged by confocal scanning laser microscopy. Large box is x-y scanned image; sidebars show x-z reconstruction. Image courtesy of F. Yildiz. Reprinted from Yildiz et al. (2004) with permission of Blackwell Publishing.
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Color Plate 15 (Chapter 23)
(A) Micrograph of V. cholerae colonizing the suckling mouse intestine. First image shows villous architecture within the small intestine; inset is a magnification of crypts within the first image detailing V. cholerae cells in intimate contact with epithelial cells. Image courtesy of M. Neal Guentzel. (B) Biofilm structures of green fluorescent protein-expressing V. cholerae as imaged by confocal scanning laser microscopy. Large box is x-y scanned image; sidebars show x-z reconstruction. Image courtesy of F. Yildiz. Reprinted from Yildiz et al. (2004) with permission of Blackwell Publishing.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch23cp16
Color Plate 16 (Chapter 23)
Microarray analysis of whole-genome transcription profiling of V. cholerae. In cluster analysis, green corresponds to downregulated expression, and red corresponds to upregulated expression. (A) Cluster analysis of smooth-rugose and rugose-rugose vpsR strains, detailing changes in vps transcription. Image courtesy of F. Yildiz. Reprinted from Yildiz et al. (2001) with permission of Blackwell Publishing. (B) Cluster analysis of rpoN, flrA, flrC, and fliA strains, demonstrating class II, class III, and class IV patterns of flagellar transcription. Image courtesy of K. Klose and F. Yildiz. (C) Venn diagram representing toxR-, tcpP-, and toxT-dependent genes, as determined by microarray analysis. Image courtesy of J. Bina and J. Mekalanos. Reprinted from Bina et al. (2003) with permission of Proceedings of the National Academy of Sciences USA.
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Color Plate 16 (Chapter 23)
Microarray analysis of whole-genome transcription profiling of V. cholerae. In cluster analysis, green corresponds to downregulated expression, and red corresponds to upregulated expression. (A) Cluster analysis of smooth-rugose and rugose-rugose vpsR strains, detailing changes in vps transcription. Image courtesy of F. Yildiz. Reprinted from Yildiz et al. (2001) with permission of Blackwell Publishing. (B) Cluster analysis of rpoN, flrA, flrC, and fliA strains, demonstrating class II, class III, and class IV patterns of flagellar transcription. Image courtesy of K. Klose and F. Yildiz. (C) Venn diagram representing toxR-, tcpP-, and toxT-dependent genes, as determined by microarray analysis. Image courtesy of J. Bina and J. Mekalanos. Reprinted from Bina et al. (2003) with permission of Proceedings of the National Academy of Sciences USA.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch24cp17
Color Plate 17 (Chapter 24)
Type III secretion system (TTSS). The type III secretion system is a protein secretion apparatus of gram-negative bacteria. Through this machinery, bacteria can inject their own proteins (effectors) into the cytosol of target eukaryotic cells (Hueck, 1998). Bacterial pathogens that cause disease by intimate interactions with eukaryotic cells, such as Salmonella, Shigella, Yersinia, and plant pathogens, have this system.
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Color Plate 17 (Chapter 24)
Type III secretion system (TTSS). The type III secretion system is a protein secretion apparatus of gram-negative bacteria. Through this machinery, bacteria can inject their own proteins (effectors) into the cytosol of target eukaryotic cells (Hueck, 1998). Bacterial pathogens that cause disease by intimate interactions with eukaryotic cells, such as Salmonella, Shigella, Yersinia, and plant pathogens, have this system.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch27cp18
Color Plate 18 (Chapter 27)
Countries/areas reporting cholera cases in 2003. This map was adapted from the map published in the Weekly Epidemiological Record, 30 July 2004: World Health Organization (2004). Cholera, 2003. Wkly. Epidemiol. Rec.
79:281–288.
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Color Plate 18 (Chapter 27)
Countries/areas reporting cholera cases in 2003. This map was adapted from the map published in the Weekly Epidemiological Record, 30 July 2004: World Health Organization (2004). Cholera, 2003. Wkly. Epidemiol. Rec. 79:281–288.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/10.1128/9781555815714.ch02back01.ch27cp19
Color Plate 19 (Chapter 27)
Schematic diagram showing involvement of environmental and host factors in the occurrence of seasonal epidemics in an area of endemic cholera. Following blooms of diverse vibrios due to environmental factors, enrichment of pathogenic V. cholerae strains occurs in humans with asymptomatic infection prior to a seasonal epidemic. Red circles represent V. cholerae strains with epidemic potential, whereas other circles represent diverse environmental V. cholerae populations.
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Click to view
Color Plate 19 (Chapter 27)
Schematic diagram showing involvement of environmental and host factors in the occurrence of seasonal epidemics in an area of endemic cholera. Following blooms of diverse vibrios due to environmental factors, enrichment of pathogenic V. cholerae strains occurs in humans with asymptomatic infection prior to a seasonal epidemic. Red circles represent V. cholerae strains with epidemic potential, whereas other circles represent diverse environmental V. cholerae populations.
Citation:
Thompson F, Austin B, Swings J.
2006.
Color Plates,
In
The Biology of Vibrios.
ASM Press, Washington, DC.
/content/book/10.1128/9781555815714.ch02back01
pub_author,pub_editor
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