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Journal of Bacteriology, February 2004, p. 903-909, Vol. 186, No. 4
0021-9193/04/$08.00+0 DOI: 10.1128/JB.186.4.903-909.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037,1 Merck & Co., Rahway, New Jersey 07065-09002
| INTRODUCTION |
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Among the 292 abstracts submitted, 84 were selected to be presented in 1 of the 10 oral sessions that characterized this year's meeting. Each session focused on a topic of general interest such as genomics, functional genomics, pathogenesis, signal transduction, regulation, and others. This brief overview of the presentations will not do justice to the many other excellent talks and posters that we could not describe here. However, some of these presentations not described in this meeting report are published in this issue of the Journal.
| GENOMICS |
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Genome variability is also a characteristic of enterococci, as pointed out by Ågot Aakra (University of Norway, Åas), who compared multiple genomes of Enterococcus faecium containing a large number of mobile elements. Diversity among these may explain the phenotypical diversity among the various strains, in particular in relation to antibiotic resistance.
The comparative genomic analysis carried out by Joseph Ferretti (University of Oklahoma, Oklahoma City) also pointed out the high degree of sequence heterogeneity due to mobile elements (bacteriophages, insertion sequence elements, transposons, and plasmids, all found in various streptococci sequenced to date). Horizontal gene transfer and chromosomal rearrangements thus can greatly contribute to increase the pathogenic potential of a given microorganism in a widely variable fashion.
Genome variability due to prophage sequences and genome rearrangements were also described by Roland Siezen for Lactobacillus species. Lactobacilli, a genus of the lactic acid bacteria branch of low G+C content, are human commensals of medical and industrial importance. Comparison of the genome sequence of Lactobacillus plantarum with other lactobacilli (L. johnsonii and L. gasseri) or other low-G+C gram-positive microorganisms (Bacillus subtilis, Listeria monocytogenes) suggested that many extra genes found in this organism may provide for its environmental flexibility and adaptability as a result of a series of functions concentrated within a unique and defined genomic region designated the lifestyle adaptation region (21).
Comparative genomics between Clostridium tetani, the causative agent of tetanus disease and the producer of the second most poisonous toxin known, Clostridium perfringens, the causative agent of gas gangrene, and C. acetobutylicum, a nonpathogenic solvent producer, was the subject of Gerhard Gottschalk's presentation (Georg-August University, Göttingen, Germany). Pathway reconstruction studies revealed the unique and remarkable capacity of C. tetani to rely on extensive sodium ion bioenergetics. Furthermore, although so-called pathogenicity islands or mobile elements flanking regions containing virulence genes were not detected in this organism, many putative virulence factors were identified, both on the chromosome and on the 74-kb plasmid, pE88. Some of these factors are common to other clostridia and other pathogenic bacteria (tetanolysin, collagenase, hemolysin, fibronecting binding proteins, and internalin), while surface layer proteins seem to be unique to C. tetani, as they are absent in C. perfringens and C. difficile. Despite all the sequence information, the mechanism regulating tetanus toxin production remains unclear: candidate regulators have been identified as two-component systems and alternative sigma factors, but their involvement, or lack thereof, still needs to be experimentally defined (6).
A complex regulatory pathway for the production of the botulinum neurotoxin was also apparent from the presentation of Eric Johnson (University of Wisconsin-Madison, Madison), although the sequences of the toxin gene clusters becoming available will help in the identification of putative regulators and allow their experimental assessment (10).
The number of presentations focused on functional genomic approaches, either global or convergent to characterization of unknown genes, was clearly indicative of the fact that we now are in a postgenomic era. The global approach was mainly carried out by means of transcription analysis in order to identify the regulon controlled by a given regulator. Thus, Theresa M. Koehler (University of Texas, Houston) revealed an extensive regulatory network controlled by the AtxA and AcpA proteins of Bacillus anthracis, originally identified for their roles in toxin and capsule production in this organism. The results revealed how AtxA is a more relevant regulator than previously assumed as its functions extends to genes on both virulence plasmids (pXO1 and pXO2) and on the chromosome. These results brought to the field of B. anthracis study the realization that the assumptions often made regarding reduced virulence of strains harboring single plasmids will need to be reassessed in view of the interconnected effect that each regulator has on the overall physiology of the organism (4).
Transcriptome analysis of L. monocytogenes for the identification of the genes regulated by the PrfA virulence factor was presented by Carmen Buchrieser (Institut Pasteur, Paris, France). PrfA is a member of the Crp/Fnr family of transcriptional regulators, and it is known to activate several key virulence genes mainly controlling cell entry, cell-to-wall spread, lysis of the vacuole, and intracellular movement. Additional genes controlled by PrfA have now been identified and classified into three groups, each differentially regulated during the infection process or in different isolates, with PrfA showing either activation or repression activity. Furthermore, an interplay between PrfA and the SigB regulon controlling the general stress response was identified from the analysis of the group III genes (29).
More on global transcriptome came from Hanne Jarmer (Technical University of Denmark, Lyngby), whose analysis of the TnrA-GlnA system for nitrogen regulation in B. subtilis revealed a connection between amino acid uptake and degradation of purine through the previously described regulation of PucR (purine regulator) by TnrA.
An exhaustive microarray analysis of gene expression profiles during growth in various carbon sources was presented by Yasutaro Fujita (Fukuyama University, Fukuyama, Japan). The take-home lesson was that genes specifically expressed during growth on any of the slowly metabolized carbon sources were not identified. However, numerous genes specifically expressed in these growth conditions were sporulation genes: a correlation was obtained between the expression level of genes for sporulation-specific sigma factors (and sporulation efficiencies) and the doubling times of growth, with inositol, maltose, and starch generating the slowest doubling times and the most efficient sporulation rates.
The talk by Dusko Ehrlich (INRA, Jouy en Josas, France) summarized the results of the systematic inactivation of B. subtilis genes carried out by a consortium of 30 laboratories. He reported the identification of 192 out of 4,100 genes analyzed as indispensable by this or previous work and 79 genes predicted to be essential (22). Of these 271 genes, only 4% (a total of 11 genes) belong to the group of genes whose function is unknown. A collective view of a bacterial cell based on gene essentiality leads to a rather simple organism consisting of a compartment formed by a membrane and a wall, enclosing elements necessary to synthesize proteins that carry out the processes to (i) duplicate the genetic information, (ii) divide the compartment, and (iii) provide for energy. Since no transcription regulator was found to be essential, modulation of gene expression does not appear to be a requirement associated with an essential process (22).
A functional analysis focused on single-gene pathways was described by Jean-Yves Dubois (University of Groningen, Groningen, The Netherlands), who characterized the eight B. subtilis genes encoding putative cytoplasmic thioredoxin-like proteins. Only the trxA mutant showed a phenotype, as this strain was deficient in competence development and sporulation. TrxA was shown to be involved in disulfide bond formation in the ComS peptide regulating ComK activity and to be involved in improving the secretion of S
S bond-containing proteins in B. subtilis. The functional genomic studies carried out by Jean-Michel Jault's laboratory (CNRS, Grenoble, France) on the ATP-binding cassette transporter identified the yvcC gene as a new multidrug resistance (MDR)-like ABC transporter involved in drug detoxification (32). The characterization of extracytoplasmic-function sigma and anti-sigma factors from E. faecalis reported by Abdellah Benachour (University of Caen, Caen, France) identified the SigV sigma factor as being involved in the stress response during starvation, heat, ethanol, and acid pH challenges. Furthermore, the sigV gene was found to be negatively regulated by the associated asfV gene, encoding an anti-sigma factor.
The function of several "y" genes of B. subtilis was revealed by Richard Losick's presentation (Harvard University, Cambridge, Mass.). Work in his laboratory found that the sfkABCDEFGH operon (ybcOPST and ybdABDE) is involved in the production and export of a sporulation killing factor while the sdpABC operon (yvaWXY) encodes an extracellular signaling protein. The concerted action of the killing factor and the signaling protein produced by cells that have entered the sporulation pathway result in inhibition of sporulation in the cells still in vegetative phase. These cells become more sensitive to the killing factor; thus, they lyse and provide nutrients for the sporulating cells to feed on and continue growing (15).
| PATHOGENESIS |
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Two-component systems do not seem to be involved in regulation of the Mga virulence regulon of S. pyogenes based on the work presented by Kevin McIver (University of Texas, Dallas). In fact, inactivation of any of the 12 nonessential two-component systems in this organism did not affect the expression of the Mga-regulated emm gene, encoding the antiphagocytic M protein. The role of the essential two-component system VicRS, a member of the YycFG family, was not investigated for this aspect of S. pyogenes virulence (38).
In the field of Streptococcus pneumoniae pathogenesis, the group of Marie-Claude Trombe (Université Paul Sabatier, Toulouse, France) presented their findings on the interconnecting role of RegR and hyaluronidase in virulence, although the extent of the relevance of these two proteins seems to be highly variable as different strains, as well as different in vivo assay conditions, led to different conclusions (8).
A new virulence factor was identified by Marco Oggioni (Università di Siena, Siena, Italy), the ZmpC metalloprotease, found to cleave the human matrix metalloprotease 9, thus suggesting a role in S. pneumoniae infection. Some correlation between the role of the zmpC gene and its presence in clinical isolates of pneumonia-derived S. pneumoniae strains further supported the author's hypothesis (31).
The variability of streptococcal infections was discussed by Emanuel Hanski (Hebrew University, Jerusalem, Israel), who identified a locus through polymorphic-tag-length-transposon mutagenesis that affected invasiveness of group A streptococci (18). The locus exhibits high homology to quorum-sensing-controlled two-component systems, is lacking in the M1 strain SF370 and in the M14GAS strain JS95, and is known as the silABC locus. Interestingly, in the M18GAS strain MGAS8232 the authors found that a single nucleotide change resulted in the transcription of a gene named silCR on the strand opposite to the one encoding the silC gene. Production of the SilCR peptide in the S. pyogenes JS95 virulent strain resulted in protection of mice from group A streptococcal infection. It was shown that the presence of the SilCR peptide reduces the degradation of interleukin-8 (IL-8) without affecting proteolysis in general, perhaps through the SilAB-dependent control of a trypsin-like protease activity. It was proposed that reduction of IL-8 degradation would allow influx of neutrophils at the site of infection, thus favoring confinement and resolution of subcutaneous infections.
Genes relevant to gastrointestinal (GI) tract infection by L. plantarum WCFS1 have been sought by Peter Bron and colleagues (Wageningen Centre for Food Sciences, Wageningen, The Netherlands) by means of resolvase-based in vivo expression technology, R-IVET, which has been used to identify genes that are activated during pathogenesis in various bacteria. The system is based on the cre-encoded resolvase combined with the loxP target sites, and it allowed the identification of GI tract-activated promoters in a mouse model system. This system, combined with in vitro screening based on the complementation of the essential alr gene, encoding alanine racemase, for the identification of bile-induced loci resulted in the identification of two loci of unknown function activated in both assay conditions. Thus the combination of in vivo-in vitro screening has provided significant insights into the GI-tract behavior of L. plantarum (5).
A very comprehensive genomic, proteomic, and immunogenic analysis of the B. anthracis chromosome and plasmid was presented by Avigdor Shafferman (Israel Institute for Biological Research, Ness Ziona). With the purpose of identifying a new vaccine candidate against B. anthracis infection, a bioinformatic analysis was carried out on the putative open reading frames (ORFs) identified on the B. anthracis chromosome and pXO1 virulence plasmid. Genes predicted to code for surface-exposed or virulence-related proteins as well as ORFs coding for proteins of unknown function but unique to this organism were selected for in vitro-in vivo analyses. Approximately 200 chromosomally encoded proteins and 11 plasmid-encoded proteins were screened with the immune-PCR expression element for direct in vitro transcription-translation followed by immunoblotting with hyperimmune anti-B. anthracis animal sera in order to identify in vivo immunogens. Parallel proteomic analysis was also applied to validate protein expression and surface localization. All these combined approaches resulted in the identification of novel putative antigens (13 chromosome and 3 plasmid encoded) that will be evaluated as a basis for an improved vaccine (1, 2).
Of interest to the pathogenesis field was the presentation by Phil Hill (University of Nottingham, Nottingham, United Kingdom), whose development of a reporter system to monitor bacterial gene expression in a natural environment could be a powerful tool in the study of host-pathogen interactions (37). A dual reporter system expressing both the Gfp and luciferase proteins was shown to effectively allow the tracking of bacterial replication and gene expression using a Staphylococcus aureus intracellular infection model (35, 36). The same system could be applied to the study of biofilm formation, an aspect of bacterial pathogenesis of great interest given the number of reports presented at this meeting on this issue. An example was the report on the in situ visualization of the quorum-response in S. aureus biofilms by time-resolved scanning laser confocal microscopy carried out by Jeremy Yarwood and colleagues (University of Iowa, Iowa City). This was a great demonstration of the use of fluorescent reporters and state of art microscopy technology for the visualization of an intriguing physiological development apparently characterized by periodical attachment-detachment-regrowth events.
A genetic analysis of biofilm formation in S. aureus was also the subject of Iñigo Lasa's talk (Universidad Publica de Navarra, Pamplona, Spain). The results of a transposon mutagenesis analysis pointed to the SarA protein (staphylococcal accessory regulator) as essential for biofilm formation via an agr-independent mechanism in four genetically nonrelated strains (41). An additional gene was identified as involved in biofilm formation in the S. aureus bovine mastitis isolate v329. The gene named bap, for biofilm-associated protein, encodes a protein of 2,276 amino acids characterized by the presence of 13 nearly identical repeats of 86 amino acids each. Bap shows sequence and structural similarity to the Esp protein of E. faecalis, itself shown in Lasa's report to affect biofilm formation in this organism.
| SIGNAL TRANSDUCTION |
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More on eukaryotic-type kinases was presented by Simone Seror (Université Paris-Sud, Orsay, France) who demonstrated how the PrkC Ser/Thr kinase involved in development, biofilm formation, and swarming motility can autophosphorylate on eight distinct Thr residues, four of which, located on the activation loop are essential for kinase activity. Furthermore, the PrpC phosphatase was shown to use PrkC as a substrate, confirming their concerted function in regulating the phosphorylation level of yet-unknown target proteins (24).
The more widespread bacterial two-component systems for signal transduction were addressed by Sarah Dubrac (Institut Pasteur, Paris, France) and Alistair Howell (Smurfit Institute, Dublin, Ireland), whose talks both focused on the regulon controlled by the YycG/YycF essential system (19). After identifying the consensus recognition sequence for the YycF response regulator, the Pasteur group has obtained specific binding to the promoter region of four genes (ftsZ, yocH, ykvT, and tagA/tagD), although potentially a total of 10 genes could be within the B. subtilis YycG/YycF regulon, mainly involved in cell wall metabolism and membrane protein synthesis. The same analysis carried out on S. aureus revealed three genes directly bound by YycF: lytM, involved in cell wall biosynthesis, and isaA and ssa, involved in virulence (11).
Among the many B. subtilis two-component systems whose function is unknown, YvqCE is one of the most conserved in gram-positive microorganisms. The talk by Hanne-Leena Hyyryläinen (National Public Health Institute, Helsinki, Finland) revealed that this system is involved in sensing secretion stresses (induced for example by the LL-37 antimicrobial peptide or by hypersecretion of AmyQ), and the level of charge of the cell wall affects its activity. Deletion of the dlt operon, encoding the cell components for the D-alanylation of cell wall teichoic acids and lipoteichoic acids, was shown to induce YvqCE-dependent genes. The effect of dlt on YvqCE turned out to be opposite to the effect on the CssRS two-component system, previously shown to be involved in controlling secretion stress as well (20). These results prompt the question: are there other two-component systems that are affected by cell wall charge? More functional analysis will be required to answer this question.
Information on another unknown two-component system came from the talk by Junichi Sekiguchi (Shinshu University, Nagano, Japan), who revealed that the YvrGH system controls the transcription of the lytC, wprA, and wapA genes, thus controlling the autolytic functions of B. subtilis.
A structural approach to the understanding of a complex signal transduction system was described by Richard Lewis (University of Newcastle, Newcastle upon Tyne, United Kingdom). By means of transmission electron microscopy the partner-switching mechanism that regulates
B activity and the general stress response in B. subtilis were shown to involve a supramolecular complex most likely formed by six identical units, each one including the RsbR and RsbS proteins, whose function is to trap the RsbT protein in the absence of stress, thus preventing the downstream cascade of events that would activate
B (9).
| REGULATION |
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B, thus affecting the general stress response, and TnrA, thus affecting nitrogen regulation (16); and the regulatory network of the CiaR/CiaH two-component system of S. pneumoniae (Regine Hakenbeck, University of Kaiserslautern, Kaiserslautern, Germany), shown to regulate many genes involved in the biochemical makeup of the cell envelope as well as downregulate the entire regulon for competence development (25). Less global and more single gene focused were the talks by Linc Sonenshein (Tufts University, Boston, Mass.) on the CodY global regulator of stationary-phase gene expression in low-G+C gram-positive bacteria and the role of GTP in activating its repressor functions under conditions of nutrient excess. The involvement of CodY in C. difficile toxin production was also presented (30). Caroline Eschevins (University of Groningen, Groningen, The Netherlands) addressed the mystery of the heterogeneous expression of the ComK regulatory protein for competence development, providing evidence of perhaps an additional regulatory level but not answering the long-lasting question of why only 10 to 20% of cells within an entire B. subtilis population become competent. Gustavo Schujman (Universidad Nacional de Rosario, Rosario, Argentina). discovered that the ylpC gene, renamed fapR, is a transcription factor common to many gram-positive organisms, involved in the global regulation of fatty acids and phospholipid metabolism in response to the cellular pool of malonyl coenzyme A (39).
Among the additional presentations focused on specific regulatory mechanisms, remarkably novel were the ones by Brooke McDaniel (Ohio State University, Columbus), whose work on transcription termination control of the S-box system revealed that efficient termination depends on S-adenosylmethionine (SAM) and not methionine as previously thought and that SAM directly binds to the leader RNA and induces conformational changes (26). The talk by Qi Meng (University of Illinois, Urbana) also addressed transcription attenuation in the pyrimidine synthesis pathway by showing a novel molecular switch that responds to CTP concentration and determines termination (high CTP) or antitermination (low CTP) of the pyrG gene, encoding CTP synthatase (27). More on transcription antitermination came from the Putzer laboratory (CNRS, Paris, France), which for the first time was able to reconstitute in vitro the tRNA-dependent antitermination reaction using the thrS gene and tRNA Thr from B. subtilis (34). From the same laboratory, Ciarán Condon reported the functional characterization of the yqjK gene, which encodes the homologue of the RNase Z enzyme, whose function is to endonucleolytically process tRNAs lacking the CCA motif. This was the first demonstration of endonucleolytic maturation of the 3' end of tRNAs in bacteria, a process generally assumed to be exonucleolytic from studies with Escherichia coli, thus establishing a new bacterial paradigm for tRNA maturation (33).
| SPORULATION AND CELL DIVISION |
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G sigma factor requires the unprocessed pro-
E form of the
E mother cell sigma factor. Adriano Henriques (Universidade Nova de Lisboa, Oeiras, Portugal) also addressed the mechanism of activation of the
G transcription factor and described the requirement for the product of the spoIIIJ gene, a lipoprotein that seems to localize to the prespore membrane (40). Clearly, time has not made the cascade of sigma factors any easier to understand than when it was discovered more than 20 years ago (23). The processing of pro-
K, discussed by Lee Kroos (Michigan State University, East Lansing), is another case in point: he discussed the use of an efficient E. coli system for assaying pro-
K processing which allowed establishment that the BofA protein is the primary inhibitor of processing, perhaps by providing the 4th zinc ligand to the zinc metalloprotease SpoIVFB, responsible for the enzymatic event. The SpoIVFA protein was also shown to inhibit pro-
K processing by enhancing BofA activity. A later step of the sporulation process was addressed by Ligia Martins (Universidade Nova de Lisboa, Oeiras, Portugal), who discussed the biochemical and structural features of CotA, an abundant component of the outer coat layer of the spore required for resistance to hydrogen peroxide and UV light. The structure of CotA determined at 1.7 Å resolution by X-ray crystallography revealed the properties of a laccase with an enhanced thermostability, probably due to an increased packing level compared to other laccases (13).
A more global approach to the understanding of gene expression during sporulation in B. subtilis was taken by Patrick Eichenberger (Harvard University, Cambridge, Mass.), whose genome-wide analysis revealed that approximately 400 genes are expressed in the mother cell during sporulation. Specific analysis of transcription factor involvement (
E, SpoIIID,
K, and GerE) also indicated that the switch between the
E and the
K regulon is dependent upon the product of the spoIIID gene while the GerE protein is necessary for the transcription switch between early and late
K-controlled genes. Furthermore, new sporulation genes were identified, such as ybaN, ytrH, and ytrI, with a strong synergy in inhibiting sporulation when deleted (12).
A global view to sporulation aspects of B. anthracis was presented by Adam Driks (Loyola University, Maywood, Ill.) and Nicholas Bergman (University of Michigan, Ann Arbor). The former presented a comparison of assembly and composition of the spore coats between B. subtilis and B. anthracis. This analysis revealed that a number of coat proteins are common to both species but coat proteins unique to only one or the other organism have been identified that support the concept that B. subtilis and B. anthracis have more than expected differences in their physiology (7). Nick Bergman analyzed gene expression during growth and sporulation of B. anthracis by DNA microarrays, documenting patterns of transcription at 15-min intervals. The take-home lesson of his presentation was that 35.8% of the B. anthracis genome is regulated in a growth phase-specific manner and these genes are expressed in five distinct groups. Surprisingly, growth phase did not seem to play a major role in regulating the expression of virulence factors, at least under the assay conditions used.
For the cell division section, Gonçalo Real (Universidade Nova de Lisboa, Oieras, Portugal) discussed a new level of regulation of the Soj/SpoOJ (ParA/ParB) function in chromosome partitioning. The product of the divIB gene in fact was found to be involved in the correct localization of the Soj and Spo0J proteins, and it interfered with nucleoid structure and segregation. The molecular details of this effect are still unknown.
The characterization of the B. subtilis SMC complex (structural maintenance of chromosome) was the subject of the presentations by Judita Mascarenhas (Philipps-University Marburg, Marburg, Germany) and Philippe Noirot (INRA, Jouy en Josas, France). The former showed how the SMC protein localizes to discrete foci in a cell-dependent manner, and it appears to interact with different regions on the chromosome, probably condensation centers that affect the global chromosome compaction. Furthermore, SMC binds to DNA as a ring-like structure, and its localization depends on its ATPase activity and on the presence of its interacting partners, ScpA and ScpB (42). The role of these two proteins in DNA repair and transcription control was analyzed by Noirot by means of a genome-wide two-hybrid system approach aimed at the identification of additional proteins interacting with this complex. Twelve proteins were indeed identified that could link the ScpAB function in chromosome dynamics with other cellular processes through (to be proven) specific protein-protein interactions.
| THE COSTA AWARD |
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In the name of Costa, we want to wish these young investigators and all of the other ones who participated in the meeting a long and satisfactory career in science.
| FOOTNOTES |
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| REFERENCES |
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B regulons. Mol. Microbiol. 49:1477-1491.[CrossRef][Medline]
B is essential for biofilm development by Staphylococcus aureus. Mol. Microbiol. 48:1075-1087.[CrossRef][Medline]
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| Appl. Environ. Microbiol. | Infect. Immun. | Eukaryot. Cell |
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| Mol. Cell. Biol. | J. Virol. | Microbiol. Mol. Biol. Rev. |
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