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Joseph Bondy-denomy - One of the best experts on this subject based on the ideXlab platform.
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Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity
Nature Microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:The identification of the KinB–AlgB two-component system, known to modulate alginate biosynthesis, together with downstream proteins that repress the Type I-F CRISPR–Cas system in Pseudomonas aeruginosa , elucidates how bacteria control the expression of nucleolytic host defence systems to minimize the potential risks of self-targeting. CRISPR–Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection^ 1 . To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases^ 2 . While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR–Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB–AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis^ 3 , 4 , as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR–Cas system. Downstream of KinB–AlgB, activators of alginate production AlgU (a σ^E orthologue) and AlgR repress CRISPR–Cas activity during planktonic and surface-associated growth^ 5 . AmrZ, another alginate regulator^ 6 , is triggered to repress CRISPR–Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR–Cas expression and activity. This suggests that while CRISPR–Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity.
Nature microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection1. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases2. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB-AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis3,4, as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR-Cas system. Downstream of KinB-AlgB, activators of alginate production AlgU (a σE orthologue) and AlgR repress CRISPR-Cas activity during planktonic and surface-associated growth5. AmrZ, another alginate regulator6, is triggered to repress CRISPR-Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR-Cas expression and activity. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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CRISPR-Cas immunity repressed by a biofilm-activating pathway in Pseudomonas aeruginosa
2019Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB/AlgB), previously characterized in regulating Pseudomonas aeruginosa virulence and biofilm establishment, as a regulator of the biogenesis of the Type I-F CRISPR-Cas surveillance complex. Downstream of the KinB/AlgB system, activators of biofilm production AlgU (a σE orthologue) and AlgR, act as repressors of CRISPR-Cas surveillance complex expression during planktonic and surface-associated growth. AmrZ, another biofilm activator, functions as a surface-specific repressor of CRISPR-Cas activity. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme, and carry hijacked homologs of AmrZ, which are functional CRISPR-Cas repressors. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
Adair L. Borges - One of the best experts on this subject based on the ideXlab platform.
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Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity
Nature Microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:The identification of the KinB–AlgB two-component system, known to modulate alginate biosynthesis, together with downstream proteins that repress the Type I-F CRISPR–Cas system in Pseudomonas aeruginosa , elucidates how bacteria control the expression of nucleolytic host defence systems to minimize the potential risks of self-targeting. CRISPR–Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection^ 1 . To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases^ 2 . While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR–Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB–AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis^ 3 , 4 , as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR–Cas system. Downstream of KinB–AlgB, activators of alginate production AlgU (a σ^E orthologue) and AlgR repress CRISPR–Cas activity during planktonic and surface-associated growth^ 5 . AmrZ, another alginate regulator^ 6 , is triggered to repress CRISPR–Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR–Cas expression and activity. This suggests that while CRISPR–Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity.
Nature microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection1. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases2. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB-AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis3,4, as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR-Cas system. Downstream of KinB-AlgB, activators of alginate production AlgU (a σE orthologue) and AlgR repress CRISPR-Cas activity during planktonic and surface-associated growth5. AmrZ, another alginate regulator6, is triggered to repress CRISPR-Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR-Cas expression and activity. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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CRISPR-Cas immunity repressed by a biofilm-activating pathway in Pseudomonas aeruginosa
2019Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB/AlgB), previously characterized in regulating Pseudomonas aeruginosa virulence and biofilm establishment, as a regulator of the biogenesis of the Type I-F CRISPR-Cas surveillance complex. Downstream of the KinB/AlgB system, activators of biofilm production AlgU (a σE orthologue) and AlgR, act as repressors of CRISPR-Cas surveillance complex expression during planktonic and surface-associated growth. AmrZ, another biofilm activator, functions as a surface-specific repressor of CRISPR-Cas activity. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme, and carry hijacked homologs of AmrZ, which are functional CRISPR-Cas repressors. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
Pieter-jan Ceyssens - One of the best experts on this subject based on the ideXlab platform.
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The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae
PLoS ONE, 2015Co-Authors: Marine Henry, Pieter-jan Ceyssens, Louis-marie Bobay, Anne Chevallereau, Emilie Saussereau, Laurent DebarbieuxAbstract:In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their ge-nomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron mi-croscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.
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Host RNA polymerase inhibitors encoded by ϕKMV-like phages of Pseudomonas.
Virology, 2012Co-Authors: Evgeny Klimuk, Pieter-jan Ceyssens, Rob Lavigne, Natalia Akulenko, Kira S. Makarova, Ivan A. Volchenkov, Konstantin SeverinovAbstract:Escherichia coli bacteriophage T7 is a founding member of a large clade of podoviruses encoding a single-subunit RNA polymerase (RNAP). phages of the family rely on host RNAP for transcription of early viral genes; viral RNAP transcribes non-early viral genes. T7 and its close relatives encode an inhibitor of host RNAP, the gp2 protein. Gp2 is essential for phage development and ensures that host RNAP does not interfere with viral RNAP transcription at late stages of infection. Here, we identify host RNAP inhibitors encoded by a subset of T7 clade phages related to ϕKMV phage of Pseudomonas aeruginosa. We demonstrate that these proteins are functionally identical to T7 gp2 in vivo and in vitro. The ability of some Pseudomonas phage gp2-like proteins to inhibit RNAP is modulated by N-terminal domains, which are absent from the T7 phage homolog. This finding indicates that Pseudomonas phages may use external or internal cues to initiate inhibition of host RNAP transcription and that gp2-like proteins from these phages may be receptors of these cues.
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Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the "N4-like viruses"
Virology, 2010Co-Authors: Pieter-jan Ceyssens, Andrew D. Brabban, Larissa Rogge, Matthew Spooner Lewis, Derek Pickard, David Goulding, Gordon Dougan, Jean-paul Noben, Andrew M. Kropinski, Elizabeth KutterAbstract:We present a detailed analysis of the genome architecture, structural proteome and infection-related properties of three Pseudomonas phages, designated LUZ7, LIT1 and PEV2. These podoviruses encapsulate 72.5 to 74.9 kb genomes and lyse their host after 25 min aerobic infection. PEV2 can successfully infect under anaerobic conditions, but its latent period is tripled, the lysis proceeds far slower and the burst size decreases significantly. While the overall genome structure of these phages resembles the well-studied coliphage N4, these Pseudomonas phages encode a cluster of tail genes which displays significant similarity to a Pseudomonasaeruginosa (cryptic) prophage region. Using ESI-MS/MS, these tail proteins were shown to be part of the phage particle, as well as ten other proteins including a giant 370 kDa virion RNA polymerase. These phages are the first described representatives of a novel kind of obligatory lytic P. aeruginosa-infecting phages, belonging to the widespread “N4-like viruses” genus.
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Pseudomonas: Model Organism, Pathogen, Cell Factory - Bacteriophages of Pseudomonas
Future microbiology, 2010Co-Authors: Pieter-jan Ceyssens, Rob LavigneAbstract:Pseudomonas species and their bacteriophages have been studied intensely since the beginning of the 20th century, due to their ubiquitous nature, and medical and ecological importance. Here, we summarize recent molecular research performed on Pseudomonas phages by reviewing findings on individual phage genera. While large phage collections are stored and characterized worldwide, the limits of their genomic diversity are becoming more and more apparent. Although this article emphasizes the biological background and molecular characteristics of these phages, special attention is given to emerging studies in coevolutionary and in therapeutic settings.
Jarosław Dastych - One of the best experts on this subject based on the ideXlab platform.
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Complete genome sequences of Aeromonas and Pseudomonas phages as a supportive tool for development of antibacterial treatment in aquaculture
Virology Journal, 2019Co-Authors: J. Kazimierczak, Ewelina Agnieszka Wójcik, Jolanta Witaszewska, Arkadiusz Guziński, Elżbieta Górecka, Edyta Kaczorek, Małgorzata Stańczyk, A. K. Siwicki, Jarosław DastychAbstract:BackgroundAquaculture is the fastest growing sector of food production worldwide. However, one of the major reasons limiting its effectiveness are infectious diseases among aquatic organisms resulting in vast economic losses. Fighting such infections with chemotherapy is normally used as a rapid and effective treatment. The rise of antibiotic resistance, however, is limiting the efficacy of antibiotics and creates environmental and human safety concerns due to their massive application in the aquatic environment. Bacteriophages are an alternative solution that could be considered in order to protect fish against pathogens while minimizing the side-effects for the environment and humans. Bacteriophages kill bacteria via different mechanisms than antibiotics, and so fit nicely into the ‘novel mode of action’ concept desired for all new antibacterial agents.MethodsThe bacteriophages were isolated from sewage water and characterized by RFLP, spectrum of specificity, transmission electron microscopy (TEM) and sequencing (WGS). Bioinformatics analysis of genomic data enables an in-depth characterization of phages and the choice of phages. This allows an optimised choice of phage for therapy, excluding those with toxin genes, virulence factor genes, and genes responsible for lysogeny.ResultsIn this study, we isolated eleven new bacteriophages: seven infecting Aeromonas and four infecting Pseudomonas, which significantly increases the genomic information of Aeromonas and Pseudomonas phages. Bioinformatics analysis of genomic data, assessing the likelihood of these phages to enter the lysogenic cycle with experimental data on their specificity towards large number of bacterial field isolates representing different locations.ConclusionsFrom 11 newly isolated bacteriophages only 6 (25AhydR2PP, 50AhydR13PP, 60AhydR15PP, 22PfluR64PP, 67PfluR64PP, 71PfluR64PP) have a potential to be used in phage therapy due to confirmed lytic lifestyle and absence of virulence or resistance genes.
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Complete genome sequences of Aeromonas and Pseudomonas phages as a supportive tool for development of antibacterial treatment in aquaculture
Virology journal, 2019Co-Authors: J. Kazimierczak, Ewelina Agnieszka Wójcik, Jolanta Witaszewska, Elżbieta Górecka, Edyta Kaczorek, A. K. Siwicki, Arkadiusz Guzinski, Małgorzata Stańczyk, Jarosław DastychAbstract:Aquaculture is the fastest growing sector of food production worldwide. However, one of the major reasons limiting its effectiveness are infectious diseases among aquatic organisms resulting in vast economic losses. Fighting such infections with chemotherapy is normally used as a rapid and effective treatment. The rise of antibiotic resistance, however, is limiting the efficacy of antibiotics and creates environmental and human safety concerns due to their massive application in the aquatic environment. Bacteriophages are an alternative solution that could be considered in order to protect fish against pathogens while minimizing the side-effects for the environment and humans. Bacteriophages kill bacteria via different mechanisms than antibiotics, and so fit nicely into the ‘novel mode of action’ concept desired for all new antibacterial agents. The bacteriophages were isolated from sewage water and characterized by RFLP, spectrum of specificity, transmission electron microscopy (TEM) and sequencing (WGS). Bioinformatics analysis of genomic data enables an in-depth characterization of phages and the choice of phages. This allows an optimised choice of phage for therapy, excluding those with toxin genes, virulence factor genes, and genes responsible for lysogeny. In this study, we isolated eleven new bacteriophages: seven infecting Aeromonas and four infecting Pseudomonas, which significantly increases the genomic information of Aeromonas and Pseudomonas phages. Bioinformatics analysis of genomic data, assessing the likelihood of these phages to enter the lysogenic cycle with experimental data on their specificity towards large number of bacterial field isolates representing different locations. From 11 newly isolated bacteriophages only 6 (25AhydR2PP, 50AhydR13PP, 60AhydR15PP, 22PfluR64PP, 67PfluR64PP, 71PfluR64PP) have a potential to be used in phage therapy due to confirmed lytic lifestyle and absence of virulence or resistance genes.
Veronica Escalante - One of the best experts on this subject based on the ideXlab platform.
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Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity
Nature Microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:The identification of the KinB–AlgB two-component system, known to modulate alginate biosynthesis, together with downstream proteins that repress the Type I-F CRISPR–Cas system in Pseudomonas aeruginosa , elucidates how bacteria control the expression of nucleolytic host defence systems to minimize the potential risks of self-targeting. CRISPR–Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection^ 1 . To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases^ 2 . While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR–Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB–AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis^ 3 , 4 , as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR–Cas system. Downstream of KinB–AlgB, activators of alginate production AlgU (a σ^E orthologue) and AlgR repress CRISPR–Cas activity during planktonic and surface-associated growth^ 5 . AmrZ, another alginate regulator^ 6 , is triggered to repress CRISPR–Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR–Cas expression and activity. This suggests that while CRISPR–Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity.
Nature microbiology, 2020Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection1. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases2. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB-AlgB), previously characterized in the regulation of Pseudomonas aeruginosa alginate biosynthesis3,4, as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR-Cas system. Downstream of KinB-AlgB, activators of alginate production AlgU (a σE orthologue) and AlgR repress CRISPR-Cas activity during planktonic and surface-associated growth5. AmrZ, another alginate regulator6, is triggered to repress CRISPR-Cas immunity upon surface association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme and carry hijacked homologs of AmrZ that repress CRISPR-Cas expression and activity. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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CRISPR-Cas immunity repressed by a biofilm-activating pathway in Pseudomonas aeruginosa
2019Co-Authors: Adair L. Borges, Bardo Castro, Sutharsan Govindarajan, Tina Solvik, Veronica Escalante, Joseph Bondy-denomyAbstract:CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB/AlgB), previously characterized in regulating Pseudomonas aeruginosa virulence and biofilm establishment, as a regulator of the biogenesis of the Type I-F CRISPR-Cas surveillance complex. Downstream of the KinB/AlgB system, activators of biofilm production AlgU (a σE orthologue) and AlgR, act as repressors of CRISPR-Cas surveillance complex expression during planktonic and surface-associated growth. AmrZ, another biofilm activator, functions as a surface-specific repressor of CRISPR-Cas activity. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme, and carry hijacked homologs of AmrZ, which are functional CRISPR-Cas repressors. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
