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_:vb376136743 _:vb376136736 _:vb376136737 _:vb376136738 _:vb376136739 _:vb376136764 _:vb376136765 _:vb376136766 _:vb376136767 _:vb376136760 _:vb376136761 _:vb376136762 _:vb376136763 _:vb376136756 _:vb376136757 _:vb376136758 _:vb376136759 _:vb376136752 _:vb376136753 _:vb376136754 _:vb376136755 _:vb376136780 _:vb376136781 _:vb376136782 _:vb376136783 _:vb376136776 _:vb376136777 _:vb376136778 _:vb376136779 _:vb376136772 _:vb376136773 _:vb376136774 _:vb376136775 _:vb376136768 _:vb376136769 _:vb376136770 _:vb376136771 _:vb376136796 _:vb376136797 _:vb376136798 _:vb376136799 _:vb376136792 _:vb376136793 _:vb376136794 _:vb376136795 _:vb376136788 _:vb376136789 _:vb376136790 _:vb376136791 _:vb376136784 _:vb376136785 _:vb376136786 _:vb376136787 _:vb376136812 _:vb376136813 _:vb376136814 _:vb376136815 _:vb376136808 _:vb376136809 _:vb376136810 _:vb376136811 _:vb376136804 _:vb376136805 _:vb376136806 _:vb376136807 _:vb376136800 _:vb376136801 _:vb376136802 _:vb376136803 _:vb376136828 _:vb376136829 _:vb376136830 _:vb376136831 _:vb376136824 _:vb376136825 _:vb376136826 _:vb376136827 _:vb376136820 _:vb376136821 _:vb376136822 _:vb376136823 _:vb376136816 _:vb376136817 _:vb376136818 _:vb376136819 _:vb376136844 _:vb376136845 _:vb376136846 _:vb376136847 _:vb376136840 _:vb376136841 _:vb376136842 _:vb376136843 _:vb376136836 _:vb376136837 _:vb376136838 _:vb376136839 _:vb376136832 _:vb376136833 _:vb376136834 _:vb376136835 _:vb376136852 _:vb376136853 _:vb376136854 _:vb376136848 _:vb376136849 _:vb376136850 _:vb376136851
n3:pmcid: PMC0
bibo:doi: 10.1371%2Fjournal.ppat.1000052
n10:contains: _:vb3471530 _:vb3471454 _:vb3471437 _:vb3471477

Subject Item: _:vb3471437
rdf:type: n10:Section
dc:title: introduction
n10:contains: _:vb3471440 _:vb3471441 _:vb3471442 _:vb3471443 _:vb3471444 _:vb3471445 _:vb3471446 _:vb3471447 _:vb3471448 _:vb3471449 _:vb3471450 _:vb3471451 _:vb3471452 _:vb3471453 _:vb3471438 _:vb3471439

Subject Item: _:vb3471438
rdf:type: n3:Context
rdf:value: Most bacteria have an inherent ability to form surface-attached communities of cells called biofilms [>>1<<]. The opportunistic pathogen Staphylococcus aureus can form biofilms on many host tissues and implanted medical devices often causing chronic infections [2]–[5].
n3:mentions: n2:11104821

Subject Item: _:vb3471439
rdf:type: n3:Context
rdf:value: The opportunistic pathogen Staphylococcus aureus can form biofilms on many host tissues and implanted medical devices often causing chronic infections [>>2<<]–[5]. The challenge presented by biofilm infections is the remarkable resistance to both host immune responses and available chemotherapies [6],[7], and estimates suggest that as many as 80% of chronic bacterial infections are biofilm
n3:mentions: n2:16452401

Subject Item: _:vb3471440
rdf:type: n3:Context
rdf:value: The challenge presented by biofilm infections is the remarkable resistance to both host immune responses and available chemotherapies [6],[>>7<<], and estimates suggest that as many as 80% of chronic bacterial infections are biofilm associated [8].
n3:mentions: n2:12379713

Subject Item: _:vb3471441
rdf:type: n3:Context
rdf:value: challenge presented by biofilm infections is the remarkable resistance to both host immune responses and available chemotherapies [6],[7], and estimates suggest that as many as 80% of chronic bacterial infections are biofilm associated [>>8<<]. In response to certain environmental cues, bacteria living in biofilms are capable of using active mechanisms to leave biofilms and return to the planktonic (free-living) state in which sensitivity to antimicrobials is regained [9]–[11].
n3:mentions: n2:12563302

Subject Item: _:vb3471442
rdf:type: n3:Context
rdf:value: In response to certain environmental cues, bacteria living in biofilms are capable of using active mechanisms to leave biofilms and return to the planktonic (free-living) state in which sensitivity to antimicrobials is regained [>>9<<]–[11]. Therefore an improved understanding of the molecular mechanism of biofilm detachment could facilitate the discovery of innovative treatment options.
n3:mentions: n2:15231780

Subject Item: _:vb3471443
rdf:type: n3:Context
rdf:value: In response to certain environmental cues, bacteria living in biofilms are capable of using active mechanisms to leave biofilms and return to the planktonic (free-living) state in which sensitivity to antimicrobials is regained [9]–[>>11<<]. Therefore an improved understanding of the molecular mechanism of biofilm detachment could facilitate the discovery of innovative treatment options.
n3:mentions: n2:15639625

Subject Item: _:vb3471444
rdf:type: n3:Context
rdf:value: Studies on the opportunistic pathogen Pseudomonas aeruginosa indicate that cell-to-cell communication (often termed “quorum-sensing”) is required to make a robust biofilm under some growth conditions [>>12<<]. Surprisingly, the opposite is true in S. aureus, as the presence of an active quorum-sensing impedes attachment and development of a biofilm [13],[14].
n3:mentions: n2:9535661

Subject Item: _:vb3471445
rdf:type: n3:Context
rdf:value: Surprisingly, the opposite is true in S. aureus, as the presence of an active quorum-sensing impedes attachment and development of a biofilm [>>13<<],[14]. The S. aureus quorum-sensing system is encoded by the accessory gene regulator (agr) locus and the communication molecule that it produces and senses is called an autoinducing peptide (AIP), which is an eight-residue peptide with
n3:mentions: n2:11069241

Subject Item: _:vb3471446
rdf:type: n3:Context
rdf:value: Surprisingly, the opposite is true in S. aureus, as the presence of an active quorum-sensing impedes attachment and development of a biofilm [13],[>>14<<]. The S. aureus quorum-sensing system is encoded by the accessory gene regulator (agr) locus and the communication molecule that it produces and senses is called an autoinducing peptide (AIP), which is an eight-residue peptide with the
n3:mentions: n2:12819120

Subject Item: _:vb3471447
rdf:type: n3:Context
rdf:value: gene regulator (agr) locus and the communication molecule that it produces and senses is called an autoinducing peptide (AIP), which is an eight-residue peptide with the last five residues constrained in a cyclic thiolactone ring [>>15<<]. During growth, AIP is synthesized and secreted through a poorly understood mechanism that requires multiple peptidases [16],[17].
n3:mentions: n2:9197262

Subject Item: _:vb3471448
rdf:type: n3:Context
rdf:value: During growth, AIP is synthesized and secreted through a poorly understood mechanism that requires multiple peptidases [>>16<<],[17]. Once AIP reaches a critical concentration, it binds to a surface histidine kinase receptor, initiating a regulatory cascade that controls expression of a myriad of virulence factors, such as proteases, hemolysins, and toxins [18]. A
n3:mentions: n2:17608791

Subject Item: _:vb3471449
rdf:type: n3:Context
rdf:value: During growth, AIP is synthesized and secreted through a poorly understood mechanism that requires multiple peptidases [16],[>>17<<]. Once AIP reaches a critical concentration, it binds to a surface histidine kinase receptor, initiating a regulatory cascade that controls expression of a myriad of virulence factors, such as proteases, hemolysins, and toxins [18]. A
n3:mentions: n2:15734745

Subject Item: _:vb3471450
rdf:type: n3:Context
rdf:value: Once AIP reaches a critical concentration, it binds to a surface histidine kinase receptor, initiating a regulatory cascade that controls expression of a myriad of virulence factors, such as proteases, hemolysins, and toxins [>>18<<]. A recent study by Yarwood et. al. [19] raised the possibility that the agr quorum-sensing system is involved in biofilm detachment.
n3:mentions: n2:12791129

Subject Item: _:vb3471451
rdf:type: n3:Context
rdf:value: it binds to a surface histidine kinase receptor, initiating a regulatory cascade that controls expression of a myriad of virulence factors, such as proteases, hemolysins, and toxins [18]. A recent study by Yarwood et. al. [>>19<<] raised the possibility that the agr quorum-sensing system is involved in biofilm detachment.
n3:mentions: n2:14996815

Subject Item: _:vb3471452
rdf:type: n3:Context
rdf:value: These findings correlate well with prior data indicating that agr deficient S. aureus strains form more robust biofilms compared to wild type strains [>>13<<],[14].
n3:mentions: n2:11069241

Subject Item: _:vb3471453
rdf:type: n3:Context
rdf:value: These findings correlate well with prior data indicating that agr deficient S. aureus strains form more robust biofilms compared to wild type strains [13],[>>14<<].
n3:mentions: n2:12819120

Subject Item: _:vb3471454
rdf:type: n10:Section
dc:title: materials and methods
n10:contains: _:vb3471455 _:vb3471476 _:vb3471472 _:vb3471473 _:vb3471474 _:vb3471475 _:vb3471468 _:vb3471469 _:vb3471470 _:vb3471471 _:vb3471464 _:vb3471465 _:vb3471466 _:vb3471467 _:vb3471460 _:vb3471461 _:vb3471462 _:vb3471463 _:vb3471456 _:vb3471457 _:vb3471458 _:vb3471459

Subject Item: _:vb3471455
rdf:type: n3:Context
rdf:value: Plasmid DNA was prepared from E. coli and transformed by electroporation into S. aureus RN4220 as described [>>84<<]. Plasmids were moved from RN4220 into other S. aureus strains by transduction with bacteriophage α80 [85] or by purifying the plasmid DNA and transformed by electroporation into appropriate strains. To move sspA and splABCDEF mutations
n3:mentions: n2:1521761

Subject Item: _:vb3471456
rdf:type: n3:Context
rdf:value: Plasmids were moved from RN4220 into other S. aureus strains by transduction with bacteriophage α80 [>>85<<] or by purifying the plasmid DNA and transformed by electroporation into appropriate strains.
n3:mentions: n2:1658572

Subject Item: _:vb3471457
rdf:type: n3:Context
rdf:value: To move sspA and splABCDEF mutations into appropriate genetic backgrounds, phage transduction with α80 was used as described [>>85<<]. To construct the Δaur mutation, the pKOR1-aur plasmid was used as described [16]. Fluorescence measurements with S. aureus strains containing pDB59 were performed as previously described [27].
n3:mentions: n2:1658572

Subject Item: _:vb3471458
rdf:type: n3:Context
rdf:value: To construct the Δaur mutation, the pKOR1-aur plasmid was used as described [>>16<<]. Fluorescence measurements with S. aureus strains containing pDB59 were performed as previously described [27].
n3:mentions: n2:17608791

Subject Item: _:vb3471459
rdf:type: n3:Context
rdf:value: coli DH5α-ECloning strainNoneInvitrogenAH394ER2566/ΔgshA::cat Cam [27] AH426AH394/pDnaB8–AIPIAmp [27] AH495AH394/pDnaB8–AIPIIAmp [27] AH496AH394/pDnaB8–AIPIIIAmp [27] Staphylococcus aureus RN4220Restriction mutant of 8325-4None [>>85<<] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr:
n3:mentions: n2:1658572

Subject Item: _:vb3471460
rdf:type: n3:Context
rdf:value: Cam [27] AH426AH394/pDnaB8–AIPIAmp [27] AH495AH394/pDnaB8–AIPIIAmp [27] AH496AH394/pDnaB8–AIPIIIAmp [27] Staphylococcus aureus RN4220Restriction mutant of 8325-4None [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [>>89<<] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl:
n3:mentions: n2:12218034

Subject Item: _:vb3471461
rdf:type: n3:Context
rdf:value: [27] AH495AH394/pDnaB8–AIPIIAmp [27] AH496AH394/pDnaB8–AIPIIIAmp [27] Staphylococcus aureus RN4220Restriction mutant of 8325-4None [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [>>89<<] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl:
n3:mentions: n2:12218034

Subject Item: _:vb3471462
rdf:type: n3:Context
rdf:value: [27] AH496AH394/pDnaB8–AIPIIIAmp [27] Staphylococcus aureus RN4220Restriction mutant of 8325-4None [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [>>31<<] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA:
n3:mentions: n2:2040432

Subject Item: _:vb3471463
rdf:type: n3:Context
rdf:value: [27] Staphylococcus aureus RN4220Restriction mutant of 8325-4None [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [>>15<<] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA::erm Erm [50] DU1126 sspA:
n3:mentions: n2:9197262

Subject Item: _:vb3471464
rdf:type: n3:Context
rdf:value: mutant of 8325-4None [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [>>90<<] SP6391 sspA::erm Erm [50] DU1126 sspA::tet Tet [91] MN8Δica::tet Tet [92] AH462SH1000/pDB59Cam [16] AH500SH1000/pAH9ErmThis workAH595SH1000/Δica:
n3:mentions: n2:11179322

Subject Item: _:vb3471465
rdf:type: n3:Context
rdf:value: [85] SH1000 rsbU positive derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA::erm Erm [>>50<<] DU1126 sspA::tet Tet [91] MN8Δica::tet Tet [92] AH462SH1000/pDB59Cam [16] AH500SH1000/pAH9ErmThis workAH595SH1000/Δica:
n3:mentions: n2:11119502

Subject Item: _:vb3471466
rdf:type: n3:Context
rdf:value: derivative of 8325-4, agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA::erm Erm [50] DU1126 sspA::tet Tet [>>91<<] MN8Δica::tet Tet [92] AH462SH1000/pDB59Cam [16] AH500SH1000/pAH9ErmThis workAH595SH1000/Δica:
n3:mentions: n2:11796572

Subject Item: _:vb3471467
rdf:type: n3:Context
rdf:value: agr Type INone [89] SH1001SH1000/Δagr::tet Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA::erm Erm [50] DU1126 sspA::tet Tet [91] MN8Δica::tet Tet [>>92<<] AH462SH1000/pDB59Cam [16] AH500SH1000/pAH9ErmThis workAH595SH1000/Δica::tet TetThis workAH596SH1000/pDB59+pAH9Cam, ErmThis workAH703SH1000/Δaur NoneThis workAH741SH1000/sspA:
n3:mentions: n2:12117954

Subject Item: _:vb3471468
rdf:type: n3:Context
rdf:value: Tet [89] FRI1169 agr Type INone [31] SA502A agr Type IINone [15] ATCC25923 agr Type IIINoneATCCKB600Δspl::erm Erm [90] SP6391 sspA::erm Erm [50] DU1126 sspA::tet Tet [91] MN8Δica::tet Tet [92] AH462SH1000/pDB59Cam [>>16<<] AH500SH1000/pAH9ErmThis workAH595SH1000/Δica::tet TetThis workAH596SH1000/pDB59+pAH9Cam, ErmThis workAH703SH1000/Δaur NoneThis workAH741SH1000/sspA:
n3:mentions: n2:17608791

Subject Item: _:vb3471469
rdf:type: n3:Context
rdf:value: workAH750SH1000/Δaur Δspl::erm ErmThis workAH788AH750/pDB59Cam, ErmThis workAH789AH703/pDB59CamThis workAH860SH1000/Δspl::erm sspA::tet Erm, TetThis workAH861SH1001/pDB59+pAH9Cam, ErmThis workPlasmidspDB59P3-GFP reporterAmp, Cam [>>19<<] pAH9 sarA promoter P1-RFPAmp, ErmThis workpDNAB8-AIPIAIP-I intein plasmidAmp [27] pDNAB8-AIPIIAIP-II intein plasmidAmp [27] pDNAB8-AIPIIIAIP-III intein plasmidAmp [27] pKOR1-aur aur knockout vectorAmp, Cam [16] Construction of an RFP
n3:mentions: n2:14996815

Subject Item: _:vb3471470
rdf:type: n3:Context
rdf:value: reporterAmp, Cam [19] pAH9 sarA promoter P1-RFPAmp, ErmThis workpDNAB8-AIPIAIP-I intein plasmidAmp [27] pDNAB8-AIPIIAIP-II intein plasmidAmp [27] pDNAB8-AIPIIIAIP-III intein plasmidAmp [27] pKOR1-aur aur knockout vectorAmp, Cam [>>16<<] Construction of an RFP reporter
n3:mentions: n2:17608791

Subject Item: _:vb3471471
rdf:type: n3:Context
rdf:value: from SH1000 genomic DNA with oligonucleotides (for 5′-GTTGTTAAGCTTCTGATATTTTTGACTAAACCAAATGC-3′, rev 5′-GTTGGATCCGATGCATCTTGCTCGATACATTTG-3′), digested with HindIII and BamHI, and cloned into the erythromycin shuttle plasmid pCE107 [>>19<<]. The mCherry (RFP) gene was PCR amplified from pRSET-mCherry [86] with oligonucleotides incorporating a 5′ ribosome binding site and KpnI site and a 3′ EcoRI site (for 5′-GTTGGTACCTAGGGAGGTTTTAAACATGGTGAGCAAGGGCGAGGAGG-3′, rev
n3:mentions: n2:14996815

Subject Item: _:vb3471472
rdf:type: n3:Context
rdf:value: The mCherry (RFP) gene was PCR amplified from pRSET-mCherry [>>86<<] with oligonucleotides incorporating a 5′ ribosome binding site and KpnI site and a 3′ EcoRI site (for 5′-GTTGGTACCTAGGGAGGTTTTAAACATGGTGAGCAAGGGCGAGGAGG-3′, rev 5′-GTTGAATTCTTACTTGTACAGCTCGTCCATGCC-3′).
n3:mentions: n2:15558047

Subject Item: _:vb3471473
rdf:type: n3:Context
rdf:value: To determine relative protease activities of strains, assays were performed as described previously using the Azocoll (Calbiochem) reagent [>>48<<]. For measuring protease levels in biofilm effluents, 100 mL of effluent was collected on ice (∼12 hours) after AIP addition to the biofilm medium. Cells were removed from the effluents through centrifugation and filtering, and ammonium
n3:mentions: n2:11454217

Subject Item: _:vb3471474
rdf:type: n3:Context
rdf:value: Microtiter plate biofilms were performed as described [>>87<<] except that the plates were incubated at 37°C with shaking at 200 rpm for 12 hours.
n3:mentions: n2:16040971

Subject Item: _:vb3471475
rdf:type: n3:Context
rdf:value: Flow cell biofilm experiments and confocal microscopy were performed as previously described [>>19<<]. Flow cells were inoculated with overnight cultures diluted 1:100 in sterile water and laminar flow (170 µl/min) was initiated after one hour incubation. Confocal microscopy was performed using a Radiance 2100 system (Biorad) with a Nikon
n3:mentions: n2:14996815

Subject Item: _:vb3471476
rdf:type: n3:Context
rdf:value: Biofilm biomass was quantified with the COMSTAT program [>>88<<] and percent biomass detached was calculated by subtracting biomass present at day 4 from day 2.
n3:mentions: n2:11021916

Subject Item: _:vb3471477
rdf:type: n10:Section
dc:title: results
n10:contains: _:vb3471478 _:vb3471479 _:vb3471480 _:vb3471481 _:vb3471482 _:vb3471483 _:vb3471484 _:vb3471485 _:vb3471486 _:vb3471487 _:vb3471520 _:vb3471521 _:vb3471522 _:vb3471523 _:vb3471524 _:vb3471525 _:vb3471526 _:vb3471527 _:vb3471528 _:vb3471529 _:vb3471504 _:vb3471505 _:vb3471506 _:vb3471507 _:vb3471508 _:vb3471509 _:vb3471510 _:vb3471511 _:vb3471512 _:vb3471513 _:vb3471514 _:vb3471515 _:vb3471516 _:vb3471517 _:vb3471518 _:vb3471519 _:vb3471488 _:vb3471489 _:vb3471490 _:vb3471491 _:vb3471492 _:vb3471493 _:vb3471494 _:vb3471495 _:vb3471496 _:vb3471497 _:vb3471498 _:vb3471499 _:vb3471500 _:vb3471501 _:vb3471502 _:vb3471503

Subject Item: _:vb3471478
rdf:type: n3:Context
rdf:value: Mutations in the agr quorum-sensing system are known to improve biofilm development [>>13<<],[14]. Based on these studies, it seemed probable that there is a correlation between agr activity and biofilm formation.
n3:mentions: n2:11069241

Subject Item: _:vb3471479
rdf:type: n3:Context
rdf:value: Mutations in the agr quorum-sensing system are known to improve biofilm development [13],[>>14<<]. Based on these studies, it seemed probable that there is a correlation between agr activity and biofilm formation.
n3:mentions: n2:12819120

Subject Item: _:vb3471480
rdf:type: n3:Context
rdf:value: Regassa et al. reported that growth on rich media containing glucose represses the agr system through the nonmaintained generation of low pH [>>20<<]. Interestingly, in most published flow cell biofilm studies, one commonality is the use of growth media containing or supplemented with glucose [9], [19], [21]–[24]. In our own efforts to grow S. aureus flow cell biofilms, we found a
n3:mentions: n2:1639506

Subject Item: _:vb3471481
rdf:type: n3:Context
rdf:value: Interestingly, in most published flow cell biofilm studies, one commonality is the use of growth media containing or supplemented with glucose [>>9<<], [19], [21]–[24].
n3:mentions: n2:15231780

Subject Item: _:vb3471482
rdf:type: n3:Context
rdf:value: Interestingly, in most published flow cell biofilm studies, one commonality is the use of growth media containing or supplemented with glucose [9], [>>19<<], [21]–[24].
n3:mentions: n2:14996815

Subject Item: _:vb3471483
rdf:type: n3:Context
rdf:value: Interestingly, in most published flow cell biofilm studies, one commonality is the use of growth media containing or supplemented with glucose [9], [19], [>>21<<]–[24]. In our own efforts to grow S. aureus flow cell biofilms, we found a strict dependence on glucose supplementation. For the experimental setup, a once-through, continuous culture system was employed as previously described [19],[25],
n3:mentions: n2:15812054

Subject Item: _:vb3471484
rdf:type: n3:Context
rdf:value: Interestingly, in most published flow cell biofilm studies, one commonality is the use of growth media containing or supplemented with glucose [9], [19], [21]–[>>24<<]. In our own efforts to grow S. aureus flow cell biofilms, we found a strict dependence on glucose supplementation. For the experimental setup, a once-through, continuous culture system was employed as previously described [19],[25], and S.
n3:mentions: n2:17452642

Subject Item: _:vb3471485
rdf:type: n3:Context
rdf:value: For the experimental setup, a once-through, continuous culture system was employed as previously described [>>19<<],[25], and S. aureus SH1000 constitutively expressing red fluorescent protein (PsarA-RFP, plasmid pAH9) was used as the testing strain.
n3:mentions: n2:14996815

Subject Item: _:vb3471486
rdf:type: n3:Context
rdf:value: For the experimental setup, a once-through, continuous culture system was employed as previously described [19],[>>25<<], and S. aureus SH1000 constitutively expressing red fluorescent protein (PsarA-RFP, plasmid pAH9) was used as the testing strain.
n3:mentions: n2:8476292

Subject Item: _:vb3471487
rdf:type: n3:Context
rdf:value: In broth culture and biofilm effluents, we observed a glucose-dependent pH decrease to the 5.5 range similar as previously reported [>>20<<],[26]. As a control, flow cell biofilms were prepared with an agr mutant strain (SH1001, Δagr::TetM) containing plasmid pAH9 (Figure 1C & D), and this strain developed a biofilm even in the absence of media supplementations (Figure 1C). As
n3:mentions: n2:1639506

Subject Item: _:vb3471488
rdf:type: n3:Context
rdf:value: In broth culture and biofilm effluents, we observed a glucose-dependent pH decrease to the 5.5 range similar as previously reported [20],[>>26<<]. As a control, flow cell biofilms were prepared with an agr mutant strain (SH1001, Δagr::TetM) containing plasmid pAH9 (Figure 1C & D), and this strain developed a biofilm even in the absence of media supplementations (Figure 1C). As
n3:mentions: n2:15576791

Subject Item: _:vb3471489
rdf:type: n3:Context
rdf:value: The flow cell media was supplemented with glucose to attenuate agr expression [>>20<<], allowing cell attachment and biofilm development.
n3:mentions: n2:1639506

Subject Item: _:vb3471490
rdf:type: n3:Context
rdf:value: The activating signals of each group cross-inhibits the alternative signal receptors with surprising potency, a phenomenon termed “bacterial interference” [>>15<<]. Since AIP-I and AIP-IV differ by only one amino acid and function interchangeably [28], they are grouped together in the classification scheme, although this assignment has been controversial [29],[30].
n3:mentions: n2:9197262

Subject Item: _:vb3471491
rdf:type: n3:Context
rdf:value: Since AIP-I and AIP-IV differ by only one amino acid and function interchangeably [>>28<<], they are grouped together in the classification scheme, although this assignment has been controversial [29],[30].
n3:mentions: n2:11053400

Subject Item: _:vb3471492
rdf:type: n3:Context
rdf:value: Since AIP-I and AIP-IV differ by only one amino acid and function interchangeably [28], they are grouped together in the classification scheme, although this assignment has been controversial [>>29<<],[30].
n3:mentions: n2:12854080

Subject Item: _:vb3471493
rdf:type: n3:Context
rdf:value: Since AIP-I and AIP-IV differ by only one amino acid and function interchangeably [28], they are grouped together in the classification scheme, although this assignment has been controversial [29],[>>30<<].
n3:mentions: n2:11489134

Subject Item: _:vb3471494
rdf:type: n3:Context
rdf:value: The strains tested were (i) FRI1169, agr-I, toxic shock syndrome isolate [>>31<<]; (ii) SA502a (ATCC27217), nasal isolate and prototype agr-II strain [15],[32]; and (iii) ATCC25923, clinical agr-III isolate [9].
n3:mentions: n2:2040432

Subject Item: _:vb3471495
rdf:type: n3:Context
rdf:value: The strains tested were (i) FRI1169, agr-I, toxic shock syndrome isolate [31]; (ii) SA502a (ATCC27217), nasal isolate and prototype agr-II strain [>>15<<],[32]; and (iii) ATCC25923, clinical agr-III isolate [9].
n3:mentions: n2:9197262

Subject Item: _:vb3471496
rdf:type: n3:Context
rdf:value: The strains tested were (i) FRI1169, agr-I, toxic shock syndrome isolate [31]; (ii) SA502a (ATCC27217), nasal isolate and prototype agr-II strain [15],[>>32<<]; and (iii) ATCC25923, clinical agr-III isolate [9].
n3:mentions: n2:13977323

Subject Item: _:vb3471497
rdf:type: n3:Context
rdf:value: The strains tested were (i) FRI1169, agr-I, toxic shock syndrome isolate [31]; (ii) SA502a (ATCC27217), nasal isolate and prototype agr-II strain [15],[32]; and (iii) ATCC25923, clinical agr-III isolate [>>9<<]. When the correct AIP signal was added to 2-day old biofilms of each strain (FRI1169, AIP-1; SA502a, AIP-II; ATCC25923, AIP-III), signal addition resulted in robust detachment of each biofilm over a period of 48 hours (Figure 3). These
n3:mentions: n2:15231780

Subject Item: _:vb3471498
rdf:type: n3:Context
rdf:value: Biofilm growth of S. aureus increases resistance to antimicrobials when compared to the planktonic growth mode [>>9<<],[19]. This biofilm mediated resistance hinders treatment of many chronic S. aureus biofilm related infections, including endocarditis, osteomyelitis, and indwelling medical device infections [3],[33].
n3:mentions: n2:15231780

Subject Item: _:vb3471499
rdf:type: n3:Context
rdf:value: Biofilm growth of S. aureus increases resistance to antimicrobials when compared to the planktonic growth mode [9],[>>19<<]. This biofilm mediated resistance hinders treatment of many chronic S. aureus biofilm related infections, including endocarditis, osteomyelitis, and indwelling medical device infections [3],[33].
n3:mentions: n2:14996815

Subject Item: _:vb3471500
rdf:type: n3:Context
rdf:value: This biofilm mediated resistance hinders treatment of many chronic S. aureus biofilm related infections, including endocarditis, osteomyelitis, and indwelling medical device infections [>>3<<],[33]. Therefore, we asked whether AIP-dispersed bacteria regained sensitivity to a clinically relevant antibiotic, rifampicin. To test this, we collected detached cells from an AIP-treated biofilm effluent and compared resistance to
n3:mentions: n2:14527295

Subject Item: _:vb3471501
rdf:type: n3:Context
rdf:value: This biofilm mediated resistance hinders treatment of many chronic S. aureus biofilm related infections, including endocarditis, osteomyelitis, and indwelling medical device infections [3],[>>33<<]. Therefore, we asked whether AIP-dispersed bacteria regained sensitivity to a clinically relevant antibiotic, rifampicin. To test this, we collected detached cells from an AIP-treated biofilm effluent and compared resistance to intact
n3:mentions: n2:14617746

Subject Item: _:vb3471502
rdf:type: n3:Context
rdf:value: Similar to previous antibiotic susceptibility results [>>19<<], even at the highest concentration tested (100 µg/ml), the level of rifampicin killing was <2 log units of the biofilm biomass (Figure 6).
n3:mentions: n2:14996815

Subject Item: _:vb3471503
rdf:type: n3:Context
rdf:value: The AIP-detached cells were more resistant than broth culture to comparable levels of rifampicin, suggesting parts of the detached biofilm may remain in emboli that are known to possess elevated antibiotic resistance [>>9<<]. These observations demonstrated that S. aureus cells detached from a biofilm regain susceptibility to a clinical antibiotic.
n3:mentions: n2:15231780

Subject Item: _:vb3471504
rdf:type: n3:Context
rdf:value: S. aureus is known to form biofilms through both ica-dependent and ica-independent mechanisms [>>34<<],[35]. To gain insight on the biofilm detachment mechanism, we sought to distinguish whether our S. aureus biofilms were dependent on PIA. In strain SH1000, we constructed an Δica::Tet deletion mutant (strain AH595) using generalized
n3:mentions: n2:17419768

Subject Item: _:vb3471505
rdf:type: n3:Context
rdf:value: S. aureus is known to form biofilms through both ica-dependent and ica-independent mechanisms [34],[>>35<<]. To gain insight on the biofilm detachment mechanism, we sought to distinguish whether our S. aureus biofilms were dependent on PIA. In strain SH1000, we constructed an Δica::Tet deletion mutant (strain AH595) using generalized
n3:mentions: n2:16030226

Subject Item: _:vb3471506
rdf:type: n3:Context
rdf:value: While SH1000 is a derivative of 8325-4, and there are reports that the ica locus is required for 8325-4 derived strains to make a biofilm [>>36<<], the ica locus was not required for biofilm formation under our experimental conditions.
n3:mentions: n2:10496925

Subject Item: _:vb3471507
rdf:type: n3:Context
rdf:value: Similar to our observations, an ica mutant of the clinical S. aureus isolate UAMS-1 displays no defect in microtiter and flow cell biofilm assays [>>22<<]. In contrast, when proteinase K was added to SH1000, biofilms were unable to develop in the microtiter plate format (data not shown), indicating the biofilms are forming through an ica-independent mechanism. These findings suggest that
n3:mentions: n2:15231800

Subject Item: _:vb3471508
rdf:type: n3:Context
rdf:value: In S. aureus strains that produce ica-independent biofilms, proteinase K eliminates adherence and biofilm formation [>>35<<], [37]–[39], perhaps through cleavage of surface structures.
n3:mentions: n2:16030226

Subject Item: _:vb3471509
rdf:type: n3:Context
rdf:value: In S. aureus strains that produce ica-independent biofilms, proteinase K eliminates adherence and biofilm formation [35], [>>37<<]–[39], perhaps through cleavage of surface structures.
n3:mentions: n2:17221196

Subject Item: _:vb3471510
rdf:type: n3:Context
rdf:value: In S. aureus strains that produce ica-independent biofilms, proteinase K eliminates adherence and biofilm formation [35], [37]–[>>39<<], perhaps through cleavage of surface structures.
n3:mentions: n2:17187854

Subject Item: _:vb3471511
rdf:type: n3:Context
rdf:value: S. aureus is coated with cell wall attached proteins that mediate adherence to a variety of substrates [>>40<<], and some of these adhesins, such as biofilm associated protein (BAP) and SasG are important for biofilm formation [41],[42].
n3:mentions: n2:17010697

Subject Item: _:vb3471512
rdf:type: n3:Context
rdf:value: S. aureus is coated with cell wall attached proteins that mediate adherence to a variety of substrates [40], and some of these adhesins, such as biofilm associated protein (BAP) and SasG are important for biofilm formation [>>41<<],[42]. It is also known that some surface adhesins, such as protein A and fibronectin-binding protein, are cleaved by the native S. aureus secreted proteases [43],[44]. Considering the agr system regulates the secreted proteases [45],[46],
n3:mentions: n2:17660408

Subject Item: _:vb3471513
rdf:type: n3:Context
rdf:value: S. aureus is coated with cell wall attached proteins that mediate adherence to a variety of substrates [40], and some of these adhesins, such as biofilm associated protein (BAP) and SasG are important for biofilm formation [41],[>>42<<]. It is also known that some surface adhesins, such as protein A and fibronectin-binding protein, are cleaved by the native S. aureus secreted proteases [43],[44].
n3:mentions: n2:16077127

Subject Item: _:vb3471514
rdf:type: n3:Context
rdf:value: It is also known that some surface adhesins, such as protein A and fibronectin-binding protein, are cleaved by the native S. aureus secreted proteases [>>43<<],[44]. Considering the agr system regulates the secreted proteases [45],[46], we hypothesized that increased expression of extracellular proteases could be responsible for biofilm detachment.
n3:mentions: n2:11447146

Subject Item: _:vb3471515
rdf:type: n3:Context
rdf:value: It is also known that some surface adhesins, such as protein A and fibronectin-binding protein, are cleaved by the native S. aureus secreted proteases [43],[>>44<<]. Considering the agr system regulates the secreted proteases [45],[46], we hypothesized that increased expression of extracellular proteases could be responsible for biofilm detachment.
n3:mentions: n2:9199429

Subject Item: _:vb3471516
rdf:type: n3:Context
rdf:value: Considering the agr system regulates the secreted proteases [>>45<<],[46], we hypothesized that increased expression of extracellular proteases could be responsible for biofilm detachment.
n3:mentions: n2:11717293

Subject Item: _:vb3471517
rdf:type: n3:Context
rdf:value: Considering the agr system regulates the secreted proteases [45],[>>46<<], we hypothesized that increased expression of extracellular proteases could be responsible for biofilm detachment.
n3:mentions: n2:15378746

Subject Item: _:vb3471518
rdf:type: n3:Context
rdf:value: There are 10 known extracellular proteases produced by most S. aureus strains and expression of all these enzymes is controlled by the agr system [>>18<<],[45],[46]. These 10 proteases include the metalloprotease aureolysin (aur), two cysteine proteases (scpA and sspB), and seven serine proteases (sspA (V8) and splABCDEF) [47].
n3:mentions: n2:12791129

Subject Item: _:vb3471519
rdf:type: n3:Context
rdf:value: There are 10 known extracellular proteases produced by most S. aureus strains and expression of all these enzymes is controlled by the agr system [18],[>>45<<],[46]. These 10 proteases include the metalloprotease aureolysin (aur), two cysteine proteases (scpA and sspB), and seven serine proteases (sspA (V8) and splABCDEF) [47].
n3:mentions: n2:11717293

Subject Item: _:vb3471520
rdf:type: n3:Context
rdf:value: There are 10 known extracellular proteases produced by most S. aureus strains and expression of all these enzymes is controlled by the agr system [18],[45],[>>46<<]. These 10 proteases include the metalloprotease aureolysin (aur), two cysteine proteases (scpA and sspB), and seven serine proteases (sspA (V8) and splABCDEF) [47].
n3:mentions: n2:15378746

Subject Item: _:vb3471521
rdf:type: n3:Context
rdf:value: These 10 proteases include the metalloprotease aureolysin (aur), two cysteine proteases (scpA and sspB), and seven serine proteases (sspA (V8) and splABCDEF) [>>47<<]. To elucidate what class(es) of proteases are prevalent in AIP-treated biofilms, the effluent from a detaching biofilm was assayed for protease activity in the presence of protease inhibitors or activating agents. The addition of EGTA, an
n3:mentions: n2:12437090

Subject Item: _:vb3471522
rdf:type: n3:Context
rdf:value: The addition of EGTA, an inhibitor of the metalloprotease aureolysin [>>16<<], had a negligible effect on overall protease activity (Figure 8C).
n3:mentions: n2:17608791

Subject Item: _:vb3471523
rdf:type: n3:Context
rdf:value: Lastly, the addition of DTT, a reducing agent used to activate thiol proteases [>>48<<], did not significantly change protease activity in the effluents.
n3:mentions: n2:11454217

Subject Item: _:vb3471524
rdf:type: n3:Context
rdf:value: Aur is a metalloprotease that is required to initiate a zymogen activation cascade [>>49<<],[50], starting with the V8 protease [51], which in turn activates the SspB cysteine protease [52].
n3:mentions: n2:14702415

Subject Item: _:vb3471525
rdf:type: n3:Context
rdf:value: Aur is a metalloprotease that is required to initiate a zymogen activation cascade [49],[>>50<<], starting with the V8 protease [51], which in turn activates the SspB cysteine protease [52].
n3:mentions: n2:11119502

Subject Item: _:vb3471526
rdf:type: n3:Context
rdf:value: Aur is a metalloprotease that is required to initiate a zymogen activation cascade [49],[50], starting with the V8 protease [>>51<<], which in turn activates the SspB cysteine protease [52].
n3:mentions: n2:711676

Subject Item: _:vb3471527
rdf:type: n3:Context
rdf:value: Aur is a metalloprotease that is required to initiate a zymogen activation cascade [49],[50], starting with the V8 protease [51], which in turn activates the SspB cysteine protease [>>52<<]. The activation mechanism of the ScpA cysteine protease remains unresolved [49]. In contrast to the serine protease mutations, introduction of the Δaur deletion into S. aureus reduced extracellular protease levels (Figure 10A) and did not
n3:mentions: n2:12207024

Subject Item: _:vb3471528
rdf:type: n3:Context
rdf:value: The activation mechanism of the ScpA cysteine protease remains unresolved [>>49<<]. In contrast to the serine protease mutations, introduction of the Δaur deletion into S. aureus reduced extracellular protease levels (Figure 10A) and did not affect biofilm formation (Figure 10B).
n3:mentions: n2:14702415

Subject Item: _:vb3471529
rdf:type: n3:Context
rdf:value: Considering the Spl proteases are not zymogens [>>53<<], we examined the combined effects of the Aur cascade and the Spl proteases by constructing an Δaur Δspl:
n3:mentions: n2:16516230

Subject Item: _:vb3471530
rdf:type: n10:Section
dc:title: discussion
n10:contains: _:vb3471564 _:vb3471565 _:vb3471566 _:vb3471567 _:vb3471560 _:vb3471561 _:vb3471562 _:vb3471563 _:vb3471556 _:vb3471557 _:vb3471558 _:vb3471559 _:vb3471552 _:vb3471553 _:vb3471554 _:vb3471555 _:vb3471580 _:vb3471581 _:vb3471582 _:vb3471583 _:vb3471576 _:vb3471577 _:vb3471578 _:vb3471579 _:vb3471572 _:vb3471573 _:vb3471574 _:vb3471575 _:vb3471568 _:vb3471569 _:vb3471570 _:vb3471571 _:vb3471588 _:vb3471589 _:vb3471590 _:vb3471591 _:vb3471584 _:vb3471585 _:vb3471586 _:vb3471587 _:vb3471532 _:vb3471533 _:vb3471534 _:vb3471535 _:vb3471531 _:vb3471548 _:vb3471549 _:vb3471550 _:vb3471551 _:vb3471544 _:vb3471545 _:vb3471546 _:vb3471547 _:vb3471540 _:vb3471541 _:vb3471542 _:vb3471543 _:vb3471536 _:vb3471537 _:vb3471538 _:vb3471539

Subject Item: _:vb3471531
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [>>54<<],[55], nitric oxide exposure [56], oxygen tension [57], iron salts [58], chelators [59], and signaling molecules [60]–[63].
n3:mentions: n2:15574944

Subject Item: _:vb3471532
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[>>55<<], nitric oxide exposure [56], oxygen tension [57], iron salts [58], chelators [59], and signaling molecules [60]–[63].
n3:mentions: n2:15489443

Subject Item: _:vb3471533
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [>>56<<], oxygen tension [57], iron salts [58], chelators [59], and signaling molecules [60]–[63].
n3:mentions: n2:17050922

Subject Item: _:vb3471534
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [56], oxygen tension [>>57<<], iron salts [58], chelators [59], and signaling molecules [60]–[63].
n3:mentions: n2:15659679

Subject Item: _:vb3471535
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [56], oxygen tension [57], iron salts [>>58<<], chelators [59], and signaling molecules [60]–[63].
n3:mentions: n2:16039526

Subject Item: _:vb3471536
rdf:type: n3:Context
rdf:value: The majority of studies on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [56], oxygen tension [57], iron salts [58], chelators [>>59<<], and signaling molecules [60]–[63].
n3:mentions: n2:16517655

Subject Item: _:vb3471537
rdf:type: n3:Context
rdf:value: on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [56], oxygen tension [57], iron salts [58], chelators [59], and signaling molecules [>>60<<]–[63]. Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:17050921

Subject Item: _:vb3471538
rdf:type: n3:Context
rdf:value: on biofilm detachment have focused on factors capable of initiating the process, such as nutrient availability [54],[55], nitric oxide exposure [56], oxygen tension [57], iron salts [58], chelators [59], and signaling molecules [60]–[>>63<<]. Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:16547056

Subject Item: _:vb3471539
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [>>10<<],[13],[64],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:16101996

Subject Item: _:vb3471540
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[>>13<<],[64],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:11069241

Subject Item: _:vb3471541
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[>>64<<],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:16098688

Subject Item: _:vb3471542
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[>>65<<], hydrolases [66],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:12533479

Subject Item: _:vb3471543
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [>>66<<],[67], proteases [37]–[39], and DNase [68].
n3:mentions: n2:15576769

Subject Item: _:vb3471544
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[>>67<<], proteases [37]–[39], and DNase [68].
n3:mentions: n2:12896987

Subject Item: _:vb3471545
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[67], proteases [>>37<<]–[39], and DNase [68].
n3:mentions: n2:17221196

Subject Item: _:vb3471546
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[67], proteases [37]–[>>39<<], and DNase [68].
n3:mentions: n2:17187854

Subject Item: _:vb3471547
rdf:type: n3:Context
rdf:value: Alternatively, detachment studies have addressed effector gene products that contribute to the dissolution of the biofilm, including surfactants [10],[13],[64],[65], hydrolases [66],[67], proteases [37]–[39], and DNase [>>68<<]. Here were do both, by demonstrating that the increasing AIP levels or lowering available glucose can function as a S. aureus biofilm detachment signal by activating the agr quorum-sensing system, resulting in increased levels of
n3:mentions: n2:11859186

Subject Item: _:vb3471548
rdf:type: n3:Context
rdf:value: These results are in accord with previous studies showing that agr mutants have a propensity to form biofilms [>>13<<],[14] and that cells actively expressing agr leave biofilms at a high frequency [19].
n3:mentions: n2:11069241

Subject Item: _:vb3471549
rdf:type: n3:Context
rdf:value: These results are in accord with previous studies showing that agr mutants have a propensity to form biofilms [13],[>>14<<] and that cells actively expressing agr leave biofilms at a high frequency [19]. Our findings also explain why S. aureus biofilm formation requires glucose supplementation to growth media.
n3:mentions: n2:12819120

Subject Item: _:vb3471550
rdf:type: n3:Context
rdf:value: These results are in accord with previous studies showing that agr mutants have a propensity to form biofilms [13],[14] and that cells actively expressing agr leave biofilms at a high frequency [>>19<<]. Our findings also explain why S. aureus biofilm formation requires glucose supplementation to growth media.
n3:mentions: n2:14996815

Subject Item: _:vb3471551
rdf:type: n3:Context
rdf:value: The presence of glucose is known to represses RNAIII through a nonmaintained pH decrease to ∼5.5 [>>20<<], resulting from the secretion of acidic metabolites.
n3:mentions: n2:1639506

Subject Item: _:vb3471552
rdf:type: n3:Context
rdf:value: The RNAIII repression is not due to glucose itself, but results from the mild acid conditions [>>26<<] and can be mimicked with other carbon sources, such as galactose [20], that also lower the media pH.
n3:mentions: n2:15576791

Subject Item: _:vb3471553
rdf:type: n3:Context
rdf:value: The RNAIII repression is not due to glucose itself, but results from the mild acid conditions [26] and can be mimicked with other carbon sources, such as galactose [>>20<<], that also lower the media pH.
n3:mentions: n2:1639506

Subject Item: _:vb3471554
rdf:type: n3:Context
rdf:value: In the host, many niches colonized by S. aureus are maintained in lower pH ranges, such as the skin and vaginal tract [>>26<<], colonization sites that repress agr function could promote biofilm formation.
n3:mentions: n2:15576791

Subject Item: _:vb3471555
rdf:type: n3:Context
rdf:value: Yarwood et al. demonstrated through time-course, flow cell studies that reactivation of agr does occur in a biofilm [>>19<<], presumably through autonomous AIP production that reaches local concentrations high enough to activate agr.
n3:mentions: n2:14996815

Subject Item: _:vb3471556
rdf:type: n3:Context
rdf:value: Biofilms are dynamic and dispersal is always operating [>>11<<], but accelerated detachment has been observed in response to changing environmental conditions, such as oxygen levels [57],[69], nutrient depletion [54], changing nutrient composition [55], or increased concentration of quorum-sensing
n3:mentions: n2:15639625

Subject Item: _:vb3471557
rdf:type: n3:Context
rdf:value: Biofilms are dynamic and dispersal is always operating [11], but accelerated detachment has been observed in response to changing environmental conditions, such as oxygen levels [>>57<<],[69], nutrient depletion [54], changing nutrient composition [55], or increased concentration of quorum-sensing signals [61].
n3:mentions: n2:15659679

Subject Item: _:vb3471558
rdf:type: n3:Context
rdf:value: Biofilms are dynamic and dispersal is always operating [11], but accelerated detachment has been observed in response to changing environmental conditions, such as oxygen levels [57],[69], nutrient depletion [>>54<<], changing nutrient composition [55], or increased concentration of quorum-sensing signals [61].
n3:mentions: n2:15574944

Subject Item: _:vb3471559
rdf:type: n3:Context
rdf:value: are dynamic and dispersal is always operating [11], but accelerated detachment has been observed in response to changing environmental conditions, such as oxygen levels [57],[69], nutrient depletion [54], changing nutrient composition [>>55<<], or increased concentration of quorum-sensing signals [61].
n3:mentions: n2:15489443

Subject Item: _:vb3471560
rdf:type: n3:Context
rdf:value: detachment has been observed in response to changing environmental conditions, such as oxygen levels [57],[69], nutrient depletion [54], changing nutrient composition [55], or increased concentration of quorum-sensing signals [>>61<<]. An S. aureus biofilm growing in vivo is likely to encounter a changing physiochemical environment, which could serve as a cue to induce accelerated detachment through an agr-mediated mechanism.
n3:mentions: n2:15866935

Subject Item: _:vb3471561
rdf:type: n3:Context
rdf:value: S. aureus has been reported to form biofilms through an ica-dependent mechanism suggesting that PIA could have a role in detachment [>>34<<],[36]. We observed no defect in microtiter or flow cell biofilm formation using an ica mutant of SH1000 (Figure 7).
n3:mentions: n2:17419768

Subject Item: _:vb3471562
rdf:type: n3:Context
rdf:value: S. aureus has been reported to form biofilms through an ica-dependent mechanism suggesting that PIA could have a role in detachment [34],[>>36<<]. We observed no defect in microtiter or flow cell biofilm formation using an ica mutant of SH1000 (Figure 7).
n3:mentions: n2:10496925

Subject Item: _:vb3471563
rdf:type: n3:Context
rdf:value: PIA is not a major matrix component of S. aureus biofilms, as exogenous addition of dispersin B, an N-acetyl-glucosaminidase capable of degrading PIA, has little effect on established biofilms of SH1000 and other S. aureus strains [>>70<<]. In contrast, dispersin B does detach S. epidermidis biofilms indicating a more significant role for PIA in the S. epidermidis matrix structure [70].
n3:mentions: n2:18039822

Subject Item: _:vb3471564
rdf:type: n3:Context
rdf:value: In contrast, dispersin B does detach S. epidermidis biofilms indicating a more significant role for PIA in the S. epidermidis matrix structure [>>70<<]. Our experiments with proteinase K and the S. aureus proteases indicate that some proteinaceous material is important for SH1000 biofilm integrity, and this result supports a number of recent studies demonstrating that proteases can
n3:mentions: n2:18039822

Subject Item: _:vb3471565
rdf:type: n3:Context
rdf:value: material is important for SH1000 biofilm integrity, and this result supports a number of recent studies demonstrating that proteases can inhibit biofilm formation or detach established biofilms from many S. aureus strains [>>35<<], [37]–[39]. It is not clear whether agr-mediated detachment will function in S. aureus strains that produce an ica-dependent biofilm.
n3:mentions: n2:16030226

Subject Item: _:vb3471566
rdf:type: n3:Context
rdf:value: material is important for SH1000 biofilm integrity, and this result supports a number of recent studies demonstrating that proteases can inhibit biofilm formation or detach established biofilms from many S. aureus strains [35], [>>37<<]–[39]. It is not clear whether agr-mediated detachment will function in S. aureus strains that produce an ica-dependent biofilm.
n3:mentions: n2:17221196

Subject Item: _:vb3471567
rdf:type: n3:Context
rdf:value: material is important for SH1000 biofilm integrity, and this result supports a number of recent studies demonstrating that proteases can inhibit biofilm formation or detach established biofilms from many S. aureus strains [35], [37]–[>>39<<]. It is not clear whether agr-mediated detachment will function in S. aureus strains that produce an ica-dependent biofilm.
n3:mentions: n2:17187854

Subject Item: _:vb3471568
rdf:type: n3:Context
rdf:value: Global expression analysis has shown that activation of the agr quorum-sensing system results in up-regulation of extracellular proteases (Aur, SplABCDEF, ScpA, SspAB) and down-regulation of many surface proteins [>>45<<],[46]. However, the target of these agr controlled proteases is not clear. One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm
n3:mentions: n2:11717293

Subject Item: _:vb3471569
rdf:type: n3:Context
rdf:value: Global expression analysis has shown that activation of the agr quorum-sensing system results in up-regulation of extracellular proteases (Aur, SplABCDEF, ScpA, SspAB) and down-regulation of many surface proteins [45],[>>46<<]. However, the target of these agr controlled proteases is not clear. One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm
n3:mentions: n2:15378746

Subject Item: _:vb3471570
rdf:type: n3:Context
rdf:value: One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm formation [>>41<<], [42], [71]–[73].
n3:mentions: n2:17660408

Subject Item: _:vb3471571
rdf:type: n3:Context
rdf:value: One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm formation [41], [>>42<<], [71]–[73].
n3:mentions: n2:16077127

Subject Item: _:vb3471572
rdf:type: n3:Context
rdf:value: One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm formation [41], [42], [>>71<<]–[73]. Atl is additionally known to require proteolytic processing for activation, and this processing is PMSF inhibited [74]. Other possibilities include microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), which
n3:mentions: n2:11292810

Subject Item: _:vb3471573
rdf:type: n3:Context
rdf:value: One potential target is the surface adhesins, and possible candidates include the surface proteins Atl, Bap, and SasG, all of which have reported roles in biofilm formation [41], [42], [71]–[>>73<<]. Atl is additionally known to require proteolytic processing for activation, and this processing is PMSF inhibited [74]. Other possibilities include microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), which are
n3:mentions: n2:9220008

Subject Item: _:vb3471574
rdf:type: n3:Context
rdf:value: Atl is additionally known to require proteolytic processing for activation, and this processing is PMSF inhibited [>>74<<]. Other possibilities include microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), which are important for adherence to the extracellular matrices of mammalian cells [40]. Also, the S. aureus secreted proteases
n3:mentions: n2:7816834

Subject Item: _:vb3471575
rdf:type: n3:Context
rdf:value: Other possibilities include microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), which are important for adherence to the extracellular matrices of mammalian cells [>>40<<]. Also, the S. aureus secreted proteases are known to activate lipase (Sal-1 and Sal-2) precursors [75] and process other secreted enzymes, such as staphylococcal nuclease [76],[77].
n3:mentions: n2:17010697

Subject Item: _:vb3471576
rdf:type: n3:Context
rdf:value: Also, the S. aureus secreted proteases are known to activate lipase (Sal-1 and Sal-2) precursors [>>75<<] and process other secreted enzymes, such as staphylococcal nuclease [76],[77].
n3:mentions: n2:9720246

Subject Item: _:vb3471577
rdf:type: n3:Context
rdf:value: Also, the S. aureus secreted proteases are known to activate lipase (Sal-1 and Sal-2) precursors [75] and process other secreted enzymes, such as staphylococcal nuclease [>>76<<],[77].
n3:mentions: n2:8843444

Subject Item: _:vb3471578
rdf:type: n3:Context
rdf:value: Also, the S. aureus secreted proteases are known to activate lipase (Sal-1 and Sal-2) precursors [75] and process other secreted enzymes, such as staphylococcal nuclease [76],[>>77<<].
n3:mentions: n2:893427

Subject Item: _:vb3471579
rdf:type: n3:Context
rdf:value: Surfactant-like molecules, such as δ-toxin, are induced by the agr system and may exert dispersal effects on biofilms [>>13<<],[78]. There is growing evidence that extracellular DNA (eDNA) is an important S. aureus biofilm matrix component [24],[70], and expression of staphylococcal nuclease is reported to be under control of the agr system [18]. Thus, while agr
n3:mentions: n2:11069241

Subject Item: _:vb3471580
rdf:type: n3:Context
rdf:value: Surfactant-like molecules, such as δ-toxin, are induced by the agr system and may exert dispersal effects on biofilms [13],[>>78<<]. There is growing evidence that extracellular DNA (eDNA) is an important S. aureus biofilm matrix component [24],[70], and expression of staphylococcal nuclease is reported to be under control of the agr system [18]. Thus, while agr
n3:mentions: n2:16487744

Subject Item: _:vb3471581
rdf:type: n3:Context
rdf:value: There is growing evidence that extracellular DNA (eDNA) is an important S. aureus biofilm matrix component [>>24<<],[70], and expression of staphylococcal nuclease is reported to be under control of the agr system [18].
n3:mentions: n2:17452642

Subject Item: _:vb3471582
rdf:type: n3:Context
rdf:value: There is growing evidence that extracellular DNA (eDNA) is an important S. aureus biofilm matrix component [24],[>>70<<], and expression of staphylococcal nuclease is reported to be under control of the agr system [18].
n3:mentions: n2:18039822

Subject Item: _:vb3471583
rdf:type: n3:Context
rdf:value: There is growing evidence that extracellular DNA (eDNA) is an important S. aureus biofilm matrix component [24],[70], and expression of staphylococcal nuclease is reported to be under control of the agr system [>>18<<]. Thus, while agr induced proteases are required for the detachment phenotype, the agr controlled expression of an array of factors (proteases, nuclease, surfactants) may also contribute to the biofilm detachment mechanism.
n3:mentions: n2:12791129

Subject Item: _:vb3471584
rdf:type: n3:Context
rdf:value: Quorum-sensing has been implicated in dispersal of biofilms formed by Yersinia pseudotuberculosis [>>79<<], Rhodobacter sphaeroides [80], Pseudomonas aureofaciens [81], Xanthomonas capmestris [62], and Serratia marceascens [61].
n3:mentions: n2:10510240

Subject Item: _:vb3471585
rdf:type: n3:Context
rdf:value: Quorum-sensing has been implicated in dispersal of biofilms formed by Yersinia pseudotuberculosis [79], Rhodobacter sphaeroides [>>80<<], Pseudomonas aureofaciens [81], Xanthomonas capmestris [62], and Serratia marceascens [61].
n3:mentions: n2:9393720

Subject Item: _:vb3471586
rdf:type: n3:Context
rdf:value: Quorum-sensing has been implicated in dispersal of biofilms formed by Yersinia pseudotuberculosis [79], Rhodobacter sphaeroides [80], Pseudomonas aureofaciens [>>81<<], Xanthomonas capmestris [62], and Serratia marceascens [61].
n3:mentions: n2:11526037

Subject Item: _:vb3471587
rdf:type: n3:Context
rdf:value: Quorum-sensing has been implicated in dispersal of biofilms formed by Yersinia pseudotuberculosis [79], Rhodobacter sphaeroides [80], Pseudomonas aureofaciens [81], Xanthomonas capmestris [>>62<<], and Serratia marceascens [61].
n3:mentions: n2:12960398

Subject Item: _:vb3471588
rdf:type: n3:Context
rdf:value: Quorum-sensing has been implicated in dispersal of biofilms formed by Yersinia pseudotuberculosis [79], Rhodobacter sphaeroides [80], Pseudomonas aureofaciens [81], Xanthomonas capmestris [62], and Serratia marceascens [>>61<<]. However, homoserine lactone signals play a divergent role in Pseudomonas aeuruginosa [12], Pseudomonas fluorescens [82], and Burkholderia cepacia [83], where the active versions of these quorum-sensing systems are necessary for biofilm
n3:mentions: n2:15866935

Subject Item: _:vb3471589
rdf:type: n3:Context
rdf:value: However, homoserine lactone signals play a divergent role in Pseudomonas aeuruginosa [>>12<<], Pseudomonas fluorescens [82], and Burkholderia cepacia [83], where the active versions of these quorum-sensing systems are necessary for biofilm formation and robustness under some growth conditions.
n3:mentions: n2:9535661

Subject Item: _:vb3471590
rdf:type: n3:Context
rdf:value: However, homoserine lactone signals play a divergent role in Pseudomonas aeuruginosa [12], Pseudomonas fluorescens [>>82<<], and Burkholderia cepacia [83], where the active versions of these quorum-sensing systems are necessary for biofilm formation and robustness under some growth conditions.
n3:mentions: n2:9867469

Subject Item: _:vb3471591
rdf:type: n3:Context
rdf:value: However, homoserine lactone signals play a divergent role in Pseudomonas aeuruginosa [12], Pseudomonas fluorescens [82], and Burkholderia cepacia [>>83<<], where the active versions of these quorum-sensing systems are necessary for biofilm formation and robustness under some growth conditions.
n3:mentions: n2:11535791

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