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Color Plates

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FIGURE 5

Computer-generated model of the C-terminal end of the M protein sequence (residues 371 to 441). A comparable region is found in all C-terminal-anchored surface proteins from gram-positive bacteria (see Table 1). The predicted location of this segment of the molecule is shown in the cytoplasm, membrane, and peptidoglycan. The space between the membrane and peptidoglycan (wall region) may be considered the “periplasm” of the gram-positive bacterium. The figure was generated on a Steller computer using the Quanta 2.1A program for energy minimization.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Structure conservation and models of T-cell activation complexes for streptococcal superantigens. (A) Ribbon diagrams of the crystal structures for streptococcal pyrogenic exotoxin serotypes A, C, H, J, streptococcal superantigen (SSA), and streptococcal mitogenic exotoxin-Z(SMEZ) (3, 7, 37, 115, 125). (B) Ribbon diagrams demonstrating typical antigen-mediated T-cell activation (left) (55) and modeled T-cell activation complexes for SpeA (middle) and SpeC (right). The co-crystal structures of SpeA and SpeC in complex with their respective TCR β-chains (127) and of SpeC in complex with the MHC class II through the zinc-dependent high-affinity binding domain have been determined (80). In light of recent evidence (130), it is likely that SpeC also activates T cells in a mode similar to the staphylococcal enterotoxin A model (80) where the superantigen also engages MHC class II through the generic low-affinity binding domain. The binding architecture for the generic low-affinity MHC class II binding to SpeA and SpeC is modeled using the staphylococcal enterotoxin B-MHC class II co-crystal structure (63). Note the presence of the zinc ion (magenta) coordinated in the high-affinity binding site for SpeC and that SpeA lacks this zinc site. The TCR α-chain (shown in gray) for both the SpeA and SpeC diagrams is modeled for clarity by superimposition of The α/β TCR shown on the left to the respective TCR β-chains for both superantigens. The figure was generated using Pymol (32).

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Reaction of mouse antistreptococcal MAb with human tissue section of myocardium in indirect immunefluorescence assay. Mouse IgM (20 μg/ml) was unreactive (not shown). MAbs were tested at 20 μg/ml. (From reference 50 with permission from . Copyright 1989, The American Association of Immunologists, Inc.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 4

Reactivity of antistreptococcal/antimyosin MAb 3.B6 with normal human valve endothelium and myocardium. Formalin-fixed human mitral valve (top left) and myocardium (top right) were reacted with MAb 3.B6 at 10 μg/ml. MAb 3.B6 binding was detected using biotin-conjugated antihuman antibodies and alkaline phosphatase-labeled streptavidin followed by fast red substrate. Control sections (bottom) did not react with human IgM at 10 μg/ml. (With permission from the .)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 5

Adhesion and extravasation of T lymphocytes into ARF valve in valvulitis. (A, B) Extravasation of CD4 lymphocytes (stained red) (original magnification, ×200 and ×400, respectively). (C) Extravasation of CD8 lymphocytes (stained red) into the valve through the valvular endothelium (magnification, ×200). An IgG isotype control MAb (IgG) did not react with the same valve (not shown) (magnification, ×400). (With permission from reference 117, the , University of Chicago)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Streptococcus-mediated signaling events and their implications. The cartoon illustrates reported signaling events. Some of the pathways are hypothesized on the basis of available specific reports on streptococci-mediated signaling events and established signal transduction pathways in eukaryotes. There are at least four receptors (uPAR, enolase, CD44, CD46) that directly interact with group A (GAS) surface proteins. Indirect binding to eukaryotic cells through fibronectin is likely mediated by α5β1 integrin. GAS invades host epithelial cells by two different mechanisms, either by invagination at the point of bacterial contact with host cells or by massive induction of microvilli, which form membrane ruffling for engulfment of bacteria (filopodia). Cytoskeletal rearrangements involve induction of the IP-3 kinase pathway or RAS/CDC42/tyrosine kinase activation. Some of the GAS secretory products such as SLO and NAD glycohydrolase may cooperatively make holes in eukaryotic cells and inject bacterial product in eukaryotic cells to exploit intracellular signaling events in a manner similar to the type III secretory system of gram-negative bacteria. Intracellular GAS may then direct host cells to undergo apoptosis via caspase-dependent and -independent pathways. In GAS-mediated apoptosis mitochondria seem to play a crucial role. NAD-glycohydrolase of GAS may convert NAD to ADP-ribose and/or cyclic ADP-ribose, which may then direct the host cell to undergo apoptosis through the Ca signaling pathway. Although not fully explored, transcriptional regulation of many inflammatory cytokines and apoptosis in the GAS-infected host cells may be mediated via NF-κB and JAK/STAT pathways. Histone-phosphorylation/dephosphorylation and histone acetylation/deacetylation also seem to play important roles in gene transcription in GAS-infected host cells. The induction of signaling pathways may vary depending on the cell lines, status of the cell (polarized versus nonpolarized), type of GAS strains, and growth phase. Abbreviations: ADPR-adenosine diphosphate-ribose; cADPR-cyclic ADPR; AIF-apoptosis inducing factor; Akt-AKT retroviral oncogene protein Ser/Thr kinase; APAF1-apoptosis protease activating factor-1 or CED-4; Arp2/3-actin-related protein 2 and 3; ASK1-apoptosis signal-regulating kinase 1 (also known as MEKK5); ATF2-activating transcription factor 2; BAD-Bcl-xL/Bcl-2 associated death promoter; Bid-BH-3 interacting domain death agonist that induces ICE-like proteases and apoptosis; Bcl2-B-cell lymphoma 2, which belongs to the Bcl-2 family of proteins and is known to inhibit apoptosis; BAK-Bcl-2 antagonist/killer. Bak is a pro-apoptotic protein; BAX-Bcl-2 associated x protein. Bax is as member of the Bcl-2 family and is pro-apoptotic; tBid-truncated Bid; CARD-caspase activation and recruitment domain; Caspase-cysteinyl aspartic acid-protease; CD44-human leukocyte differentiation receptor antigen for hyaluronate and proteoglycin serglycin; CD46-member of RCA gene family, receptor for measles virus and the M protein of GAS; Cdc42-cell division cycle 42 (GTP-binding protein); CytC-cytochrome C; c-Fos/c-Jun-transcription factor, also known as activator protein or AP-1; ELK1-Ets domain containing DNA-binding protein. Mammalian ELK-1, ELK-3 (also known as Net or SAP-2) and ELK-4 (also known as SRF accessory protein 1 [SAP-1]), which all form a ternary complex with the serum response factor (SRF); ERK-extracellular signal-related protein kinase; FADD-Fas-associated death domain; FAK-focal adhesion kinase; FAS-known as CD95 or APO-1. Fas is a member of the TNF receptor family and promotes apoptosis. FasL-Fas ligand. FasL is also known as APO-1 ligand or Apo-L; FLIP-FLICE (Fadd-like ICE [interleukin-1b converting enzyme also known as caspase-1]) inhibitory protein; G-G-protein α, β, and γ; HAT-histone acetyl transferase; HDAC-histone deacetylase; IKB-inhibitory IB (inhibitor of NF-κB) proteins; IKKs-IKK-1 and IKK-2 are two direct IB kinases; IL-interleukins; INF-interferon α or γ; INFR-interferon- γ receptor; IRAK-interleukin-1 receptor-associated kinases; JAK-Janus kinase; JNK-c-Jun N terminal kinase; MAPK-mitogen-activated protein kinase; MEK-MAPK activator; MEKKs-mitogen-activated protein/ERK kinase kinases; MLK1,2-CdC42-dependent kinases; MLK4,7-CdC42-dependent kinases; mTOR-mammalian target of Rapamycin (an immunosuppressant) protein; MyD88-myeloid differentiation factor 88; NAD-nicotinamide adenine dinucleotide; NFKB-nuclear factor of immunoglobulin κ locus in B cells. NF-κB activates transcription of genes in many tissues; NIK-Nck interacting kinase (interacting with MEKK) is different from NIK (NFκB-interacting kinase); PI-3K-Phosphatidyl inositol-3 kinase; RAC-small GTP-binding protein encoded by the gene; RAS-small GTP-binding protein protooncogene encoded by the gene; RIP-receptor interacting protein; ROS-reactive oxygen species; SEN, streptococcal surface enolase; SH2-Src homology region 2; SLO, streptolysin O; STAT-signal transducers and activators of transcription; TIRAP-Toll-interleukin 1 receptor domain-containing adaptor protein; TLR-Toll-like receptor; TNF-tumor necrosis factor; TNFR-tumor necrosis factor receptor; TOLL-human homologue of the Toll protein; TOLLIP-Toll-interacting protein; TRAD-TNF receptor I associated death domain; TRAF-tumor necrosis factor receptor-associated factors; SDH-streptococcal surface dehydrogenase; uPAR-urokinase plasminogen activator receptor.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 8

The late gene regions of the group IV prophages. Some of the identifiable genes are listed below the MGAS8232 phi SpeLM prophage genome; the corresponding color scheme is used to identify related genes in the other prophages. The locations of probable mutations are indicated by the box symbol.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 5

Structure of Rel1-385. (A) ppGpp Hydrolase-OFF/synthetase-ON conformation, in complex with Mn (blue sphere) and GDP (stick rendering). The hydrolase domain is highlighted in green a-helices and blue β-strands, the synthetase domain is in yellow a -helices and orange β -strands, and the central 3-helix bundle is in red. Part of the substrate-binding cleft comprising the hydrolase site (downregulated) is disordered (red arrow). The small synthetase/hydrolase interdomain contact interface involved in signal transmission is labeled with a red star. (B) Hydrolase-ON/synthetase-OFF conformation, in complex with Mn, ppG′:3′p (which locks the enzyme in the hydrolase-ON/synthetase-OFF conformation) and GDP. The coloring and rendering schemes are the same as for (A). The disordered synthetase site (down-regulated) is illustrated as dashed lines with a red arrow. (C) Primary and secondary structure of Rel1-385. Secondary structure is color-coded according to (A) and (B). Unique secondary structure assignments for (A) are placed immediately below the corresponding assignments for (B). Residues absolutely conserved throughout the mono- and bifunctional RelA and SpoT homologs are underlaid with blue boxes. Residues conserved in SpoT and the bifunctional enzymes but mutated in the hydrolase-incompetent RelA homologs are underlaid with red boxes. Upright and inverted black triangles above the sequence indicate residues which, when substituted experimentally by missense mutations, lead to defective hydrolase and synthetase activities, respectively. (Reproduced from reference 51, with permission.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Immuno-histochemical and schematic depiction of the choline biology of the pneumococcal surface. Immunogold-labeling of pneumococci with (A) TEPC-15 antibody recognizing free choline and (B) antiautolysin antibody. These two images contrast free (A) versus CBP-bound (B) choline. (C) Schematic view of the capsule (blue), cell wall (green), and membrane (red). The teichoic and lipoteichoic acids are indicated as dark blue lines bearing choline (circles). A proportion of these are capped by CBPs. (Courtesy of Dr. K. G. Murti, St. Jude Electron Microscopy Core Facility.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Organization of the VanA and VanB vancomycin resistance systems. Gene functions are color-coded: green, sensory and regulatory; red, essential resistance genes; blue, auxiliary resistance genes. Detailed functions of each gene are described in the text. Green arrows show the position of the VanR-inducible promoters. The percent identity of the VanB genes to their VanA homologs is given below the individual VanB genes. Homologs have identical names in both systems except for the and ligases.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 2

Regulatory circuitry of the pheromone response. (A) Events occurring at the cell surface. Important chromosomally encoded determinants are colored yellow, with the exception of the pheromone itself, which is shown as blue circles. Plasmid-encoded determinants are color-coordinated with their genes shown in B. The inhibitor peptide (ip) is shown as red circles and competitively inhibits pheromone binding to TraC. TraB inhibition of pheromone secretion is depicted here as sequestration, but this is only one possible mechanism and has not been proven. (B) Events occurring at the DNA level. Binding of pheromone by TraA links events at the cell surface with events at the DNA level. A conformational change in TraA due to pheromone binding is indicated by the change in shape of the molecule and change in dimerization state, although the precise changes are still unknown. Pheromone-free TraA binds P0 and inhibits transcription. Direction of transcription from P0 and Pa is indicated by the arrows. The antisense RNA, generalized to aR in this figure, stimulates termination at t1, indicated by the green arrow. Positive regulatory elements vary between different pheromone-responsive plasmids, and their mechanisms of inducing downstream transcription of the conjugation structural genes may also vary. For simplicity, the more common gene names and order are used. It should be noted that the gene order of the and genes is reversed in pAD1. The RepA gene is shown to orient the reader relative to Fig. 3. (C) Events at the RNA level. Relative levels of RNA produced from the P and P promoters under uninduced (red) and induced (green) conditions are depicted by the size of the arrows.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 4

Model of RNA I-RNA II interaction. RNA I is the larger black structure and RNA II is the smaller blue structure. Stems, loops, and bulges are depicted in their approximate locations and sizes as determined by experimentation. The red stem-loop structure within RNA I sequesters the ribosomebinding site and prevents translation until a complex is formed. The initial interaction occurs at a U-turn motif in the terminator loop of RNA I (A), followed by interaction between the complementary repeats in the 5′ end of each RNA (B and C). Because RNA II-mediated protection from the RNA I-encoded toxin occurs in vivo even when one of the repeats is mutated, the structure shown in panel C is apparently sufficient to revent translation in vivo. Once complex formation is complete (D), the structure is extremely stable in vivo and in vitro, perhaps due to the gap between the interacting repeats.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 5

Genetic organization of Tn and the relative positions of Int and Xis binding sites. (A) Functions of Tn genes are color-coded: blue, recombination; green and red, positive and negative regulation, respectively; yellow, tetracycline resistance; magenta, conjugation. Gene names and open reading frame numbers are shown above the individual genes. The origin of transfer is designated by the line between s and labeled . Promoters and the direction of transcription are designated by labeled arrows below the gene line. (B) Binding sites for the Int-C and Int-N DNA-binding domains and Xis are designated by marked circles and triangles. Int and Xis binding sites are color-coordinated with the genes shown in panel A.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 5

Different types of SCC elements demonstrated in MRSA orf X, open reading frame X of the chromosome. (Adapted with permission from references 16 and 30.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 2

Whole genome comparisons using the bitsum method. Coding regions from each of the six sequenced strains were used in a BLASTp analysis with ORFs from NCTC 8325. The bit scores for these BLASTp comparisons were then summed (the bitsum) and used to plot the similarity of each genome to strain 8325. Coding regions from the completed genomes for other gram-positive organisms are shown for comparison.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 3

Circular map of the NCTC 8325 genome. The ORFs present on the sense strand are represented on the outermost circle, the ORFs on the antisense strand are shown on the second circle, and the innermost circle is the GC skew on each coding strand. Nucleotide positions are labeled every 200,000 bp, and each of the predicted ORFs is colored based on the assigned functional role category in the final annotation. Colors and designations for each role category can be found in the legend for Fig. 4. As is customary, the first ORF represented is .

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 4

Graphical representation of the functional role category assignments for each of the 2,892 predicted ORFs for NCTC 8325. Numbers of genes and the percentage of the genome they represent are shown for each category. Percentage and the number of ORFs total more than 100% due to multiple role assignments for some ORFs.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Staphylococcal abscesses. A) Cutaneous furuncle (Nadir Goksugur, M.D., Dermatlas; http://www.dermatlas.org). (B) Stained section of pulmonary abscess. Kindly provided by Martin Nachbar.

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 3

, and TCS modules known to affect the virulon. (A) The system. The pro-AIP peptide is processed and secreted by AgrB, binds to an extracellular loop in the receptor-HPK, AgrC, activating autophosphorylation (or dephosphorylation), followed by phosphorylation or dephosphorylation of the response regulator, AgrA. AgrA, in conjunction with SarA, activates the two promoters, P2 and P3, leading to the production of RNAIII. RNAIII controls transcription of the target genes via one or more intracellular regulatory mediators, including a second two-component module, . (B) The locus encodes a receptor-HPK () and a response regulator (), driven by a single promoter and followed by a terminator stem-loop. (C) . The locus encodes a receptor-HPK () and a response regulator (), driven by a single promoter that generates two transcripts whose relative significance is unknown. (Reprinted from reference 94 with the kind permission of Blackwell Publishing, Ltd.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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Early and persistent infiltrations of inflammatory cells during dermatitis. The micrograph shows the inflammatory infiltrate in mouse skin that was inoculated intracutaneously with 2 × 10 CFU of LS-1: after 6 h (A), 48 h (B), and 1 week (C). The inflammatory infiltrate, which mainly contains macrophages, peaks at 48 h and starts to disappear 2 weeks after the inoculation (from reference 59).

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 5

Fluorescence microscopy of Vero cells infected with wild-type (A) or ΔActA (B). Wild-type induces the formation of actin comet tails that propulse the bacteria in the host cell cytoplasm (A), while ΔActA proliferates in microcolonies that are unable to spread from the primary infected cell (B). DNA is labeled with DAPI (4′,6′-diamidino-2-phenylindole; blue), the bacterial cell wall is labeled with an anti- antibody (red), and actin is labeled with fluorescent phalloidin (green).

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 1

Ribbon diagrams representing structures of the anthrax toxin proteins. (A) Monomeric PA. Ia (blue), 20-kDa fragment removed with cleavage; Ib (yellow), forms N terminus of PA and contains two structural calcium ions (red); II (green), pore formation; III (magenta), oligomerization of PA; IV (turquoise), receptor binding. (B) LF. Substrate-binding and catalytic domains (green) and PA-binding domain (magenta). (C) EF in complex with calmodulin. Catalytic core (green); PA-binding domain (magenta); helical domain (yellow) interacts with calmodulin (red). (Courtesy of W.-J. Tang.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 2

Model of anthrax toxin action. PA binds to receptors TEM8 or CMG2. Following proteolytic cleavage of PA by furin, PA oligomerizes to form a heptameric prepore. EF-LF binds to the prepore, and the complex is endocytosed. Acidification of the intracellular compartment triggers translocation of EF and LF to the cytosol. EF, a calmodulin-dependent adenylate cyclase, converts ATP to cAMP. LF, a zinc-dependent protease, cleaves members of the MEK family and may also affect other targets. (Reprinted from Moayeri and Leppla [75].)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 2

Structure of the 2[Ni DtxR(C102D)]- operator complex. Residues 3 to 120 in each DtxR(C102D) monomer are designated “a” to “d.” Ribbons and arrows are used to indicate a-helices and β-strands in each monomer. The 33-bp DNA segment carries the 27-bp interrupted palindromic operator sequence. (Adapted from White et al. [107].)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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FIGURE 6

Confocal micrographs of nocardia-inducedapoptosis. (A) Apoptosis of dopaminergic neurons in the substantianigra in a head-shake mouse 14 days after infection.The red stain localizes dopaminergic neurons. Free 3-OH endsof DNA from apoptotic nuclei were labeled with nucleotidesconjugated to fluorescein isothiocyanate (green). (B) Uninfectedcontrol. Dopaminergic neurons in the substantia nigrain a healthy uninfected mouse. The red stain localizes dopaminergicneurons. Note that there is no apoptosis. (Reproduced from reference 68.)

Citation: Fischetti V, Novick R, Ferretti J, Portnoy D, Rood J. 2006. Color Plates, In Gram-Positive Pathogens, Second Edition. ASM Press, Washington, DC.
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