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  • 85
    MJ Research biofilm a
    Biofilm A, supplied by MJ Research, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biofilm a/product/MJ Research
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    biofilm a - by Bioz Stars, 2020-04
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    89
    Bio-Rad biofilm a
    Biofilm A, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 89/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Rayto Life biofilm
    Biofilm, supplied by Rayto Life, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Johnson & Johnson biofilms
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilms, supplied by Johnson & Johnson, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Denville Scientific blue biofilm
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Blue Biofilm, supplied by Denville Scientific, used in various techniques. Bioz Stars score: 93/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    GraphPad Prism Inc biofilm chemostats
    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The <t>biofilms</t> were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.
    Biofilm Chemostats, supplied by GraphPad Prism Inc, used in various techniques. Bioz Stars score: 95/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Fisher Scientific biofilm substratum
    The S-layer and type IV pili are required for <t>biofilm</t> formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.
    Biofilm Substratum, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 95/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Olympus biofilm distribution
    Percentage <t>biofilm</t> formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).
    Biofilm Distribution, supplied by Olympus, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Waters Corporation biofilm formation
    Internal architecture of bacterial <t>biofilms</t> on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.
    Biofilm Formation, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 92/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Innovotech biofilm inoculator
    Internal architecture of bacterial <t>biofilms</t> on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.
    Biofilm Inoculator, supplied by Innovotech, used in various techniques. Bioz Stars score: 94/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Innovotech biofilms biofilms
    Persister cells in H. volcanii <t>biofilms.</t> Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p
    Biofilms Biofilms, supplied by Innovotech, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    SAS institute biofilm control sas
    Persister cells in H. volcanii <t>biofilms.</t> Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p
    Biofilm Control Sas, supplied by SAS institute, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc biofilm cells
    Quantification of <t>biofilm</t> formation by the wild-type strain (ATCC 17978), a stable knockout mutant strain lacking the gene A1S_0114 (ATCC Δ0114), the same mutant strain containing the pET-RA plasmid (ATCC Δ0114 + PETRA), and a mutant strain containing the pET-RA plasmid harboring the A1S_0114 gene (ATCC Δ0114 + PETRA + 0114).
    Biofilm Cells, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Bitplane biofilm analysis xtension
    Quantification of <t>biofilm</t> formation by the wild-type strain (ATCC 17978), a stable knockout mutant strain lacking the gene A1S_0114 (ATCC Δ0114), the same mutant strain containing the pET-RA plasmid (ATCC Δ0114 + PETRA), and a mutant strain containing the pET-RA plasmid harboring the A1S_0114 gene (ATCC Δ0114 + PETRA + 0114).
    Biofilm Analysis Xtension, supplied by Bitplane, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Corning Life Sciences biofilm construction biofilms
    Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old <t>biofilms</t> ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error
    Biofilm Construction Biofilms, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Becton Dickinson biofilm formation biofilms
    Confocal Laser Scanning Microscopy of <t>biofilm</t> formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static <t>biofilms</t> were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100
    Biofilm Formation Biofilms, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Innovotech calgary biofilm plate
    Liposomal clarithromycin activity on P. aureginosa PA-13572 <t>biofilm</t> (MBEC assay). Free (F-CAM) or liposomal formulations were introduced to mature biofilm at concentrations of 32 mg/liter (a), 64 mg/liter (b), and 128 mg/liter (c). Untreated biofilm acted as a control. The data represent three independent experiments in triplicate and are shown as means ± SEM. P values were considered significant compared with the control: ***, P
    Calgary Biofilm Plate, supplied by Innovotech, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher filmtracer green biofilm
    Liposomal clarithromycin activity on P. aureginosa PA-13572 <t>biofilm</t> (MBEC assay). Free (F-CAM) or liposomal formulations were introduced to mature biofilm at concentrations of 32 mg/liter (a), 64 mg/liter (b), and 128 mg/liter (c). Untreated biofilm acted as a control. The data represent three independent experiments in triplicate and are shown as means ± SEM. P values were considered significant compared with the control: ***, P
    Filmtracer Green Biofilm, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Avantor biofilms
    Tracking and quantification of <t>biofilm</t> community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .
    Biofilms, supplied by Avantor, used in various techniques. Bioz Stars score: 96/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad biofilm
    Antibiofilm activity of bacteriocin on S. epidermidis <t>biofilm</t> formation as well as eradication of established biofilm at different concentrations detected by crystal violet staining assay.
    Biofilm, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 282 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Biomatik biofilms
    CiaRH is required for biofilm formation by the ΔsdbA mutant. (a) Crystal violet staining of 24 h <t>biofilms</t> grown in 24-well plates. Biofilms were grown with the parent, ΔsdbA , sdbA -complemented mutant (+SdbA), ΔciaRH , ΔsdbAΔciaRH double mutant, and ΔsdbA ciaRH -complemented mutant ( ΔsdbA + CiaRH). Results are means ± SD of at least three experiments. The lower panel shows representative wells after staining. (b) In parallel to the biofilm formation assay, three additional wells for each strain were tested for total growth. The optical density was measured for the combined biofilm and planktonic cells for each mutant. (c) Biofilm formation of single deletion mutants for ciaRH and degP in the parent strain. Biofilms were grown for 24 h in 24-well plates prior to staining. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the parent (*** P ≤ 0.001, **** P ≤ 0.0001).
    Biofilms, supplied by Biomatik, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    BioTek Instruments biofilm
    <t>Biofilm</t> production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .
    Biofilm, supplied by BioTek Instruments, used in various techniques. Bioz Stars score: 96/100, based on 128 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Carl Roth GmbH biofilms
    Cell density [log 10 (CFU/cm 2 )] of the 1 (black) and 7 (red) day(s) old dual-species <t>biofilm</t> as function of the CAP treatment time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Geeraerd et al. ( 2000 ) model are represented: total population on general medium (□, solid line), L. monocytogenes population on Palcam medium (x, dashed line), and S . Typhimurium population on XLD medium (♢, dotted line).
    Biofilms, supplied by Carl Roth GmbH, used in various techniques. Bioz Stars score: 94/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Carl Zeiss biofilms
    <t>Biofilm</t> produced by C. jejuni 81-176 on cover glass after 48 h at 37°C under microaerobic conditions and visualized by Field Emission Scanning Electron Microscopy. (A) C. jejuni 81-176 wild-type, (B) C. jejuni 81-176Δ cj0588 , (C) the complemented C. jejuni strain 81-176Δ cj0588 :: 0588 . Experiments were performed in triplicate and representative micrographs are shown.
    Biofilms, supplied by Carl Zeiss, used in various techniques. Bioz Stars score: 99/100, based on 1764 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Difco biofilm
    Staphylococcus aureus QS gene expression when co-cultured with P. aeruginosa on tube reactors. S. aureus <t>biofilms</t> were cultured in tube reactors for a period of 5 days previous to the introduction of P. aeruginosa . Once P. aeruginosa aeruginosa was introduced (day 0), samples were taken at 24 h intervals for a period of 120 h. (A) relative expression of S. aureus QS genes in dual-species biofilms compared to single species biofilms. (B) Relative expression of S. aureus single species biofilms compared to time 0. Changes of relative expression were considered significant when a twofold change was present.
    Biofilm, supplied by Difco, used in various techniques. Bioz Stars score: 96/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eppendorf AG biofilm
    Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the <t>biofilm.</t> Negative depths in the profile represent the distance from the biofilm surface into the wastewater.
    Biofilm, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 125 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Fisher Scientific biofilms
    Confocal micrograph of a <t>biofilm</t> formed in a chinchilla middle ear by NTHi strain 2019 stained with MAb 6E4. The antibody was counterstained with a goat anti-mouse anti IgG antibody conjugated to fluorescein. The DNA in the biofilm was counterstained with DAPI and fluoresces blue. Organisms can be seen throughout the biofilm stained with MAb 6E4, indicating the presence of the KDO epitope in vivo .
    Biofilms, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 94/100, based on 171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    GE Healthcare biofilms
    Biofilm development during microbial limitation. Confocal scanning micrographs of Clostridium thermocellum <t>biofilms</t> on Whatman #3 filter paper chads taken midway during the ‘biofilm invasion’ region. Low magnification images (below) show varying degrees of biofilm colonization (green) on cellulose fibers (red); where it is common to observe surface fibers with little to no biofilm growth. High magnification imaging (above) of selected heavily populated fibers shows the typical cell monolayer biofilms of this species, with cells closely lining the substratum. Dividing cells (red circles) and occasional small spore-forming cells (green dots) are observed at the surface. Cells stained with SYTO 9 (green); cellulose fibers stained with WGA-TRITC (red).
    Biofilms, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 93/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    GraphPad Prism Inc biofilm
    Cinnamomum zeylanicum Blume EO inhibitory effect on <t>biofilm</t> formation and mature biofilm reduction (G1: 24-h contact with EO; G2: 48-h contact with EO) corresponding to (a) Candida albicans ATCC 60193; (b) Candida tropicalis ATCC 750; and (c) Candida spp. multispecies ( Candida albicans ATCC 60193 and Candida tropicalis ATCC 750). ∗ Significant biofilm reduction (Kruskal-Wallis test followed by Dunn's post hoc test, p
    Biofilm, supplied by GraphPad Prism Inc, used in various techniques. Bioz Stars score: 93/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Hitachi Ltd biofilm
    The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species <t>biofilms</t> of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).
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    ibidi biofilms
    Quantitative analysis of macrophage migration within 48 h <t>biofilms</t> prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.
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    Illumina Inc biofilms
    Functional annotation of differentially expressed genes reveals upregulation of drug transporters. Gene distribution of significantly upregulated C. auris genes in 24-h <t>biofilms</t> relative to planktonic cells, grouped into biological process (BP), cellular component (CC), and metabolic function (MF) gene ontology categories (A). Log 2 fold change of upregulated ABC and MFS drug transporters within 24-h biofilms (B). All GO terms have a P value of
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    Image Search Results


    An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The biofilms were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.

    Journal: BMC Microbiology

    Article Title: High-throughput metal susceptibility testing of microbial biofilms

    doi: 10.1186/1471-2180-5-53

    Figure Lengend Snippet: An overview of the high-throughput protocol for metal susceptibility testing using the MBEC assay . (A) Frozen stocks of bacteria were streaked out on the appropriate agar medium to obtain a first- and a subsequent second-subculture. (B) Colonies were collected from second-subcultures and suspended in broth medium to a 1.0 McFarland Standard. (C) This suspension was diluted 30-fold in broth, and the 1 in 30 dilution was used to inoculate the MBEC assay. (D) The inoculated device was placed on a rocking table in an incubator. (E) Serial dilutions of metal cations and oxyanions were set up along length of a microtiter plate along (the challenge plate). (F) The biofilms were rinsed to remove loosely adherent planktonic bacteria. (G) The first peg from each row was removed. These pegs were used to verify growth of the biofilms on the pegs. The peg lid was then inserted into the challenge plate. (H) During exposure, metals diffuse into the biofilm while planktonic cells are shed from the surface of the biofilm. Sloughed cells serve as the inoculum for planktonic MIC and MBC determinations. (I) The exposed biofilms were rinsed twice and the peg lid was inserted into fresh recovery medium containing the appropriate neutralizing agent (the recovery plate). The biofilms were disrupted into the recovery medium by sonciation on a water table sonicator. (J) Aliquots of planktonic cultures were transferred from the challenge plate to a microtiter plate containing the appropriate neutralizing agents (the neutralizing plate). (K) An aliquot from the recovery and neutralizing plates were spotted onto rich agar media. (L) MIC values are determined by reading the optical density at 650 nm (OD 650 ) of the challenge plate after the desired period of incubation using a microtiter plate reader. Spot plates were qualitatively scored for growth to obtain MBC and MBEC values. MBEC values were redundantly determined by determining the A 650 of the recovery plates after incubation.

    Article Snippet: In general, biofilms formed using a trough have a 5- to 10-fold greater cell density than those formed using the microtiter plate format (J.J. Harrison, H. Ceri and C. Stremick, unpublished data).

    Techniques: High Throughput Screening Assay, Incubation

    Growth of bacterial biofilms in the MBEC assay . (A) Mean cell density of Pseudomonas aeruginosa ATCC 27853 biofilms on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.842 using one-way ANOVA). (B) SEM photomicrograph of a P. aeruginosa biofilm on the peg surface. (C) Mean cell density of Escherichia coli TG1 on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.274 using one-way ANOVA). (D) SEM photomicrograph of an E. coli biofilm on the peg surface. The bar represents 5 μm.

    Journal: BMC Microbiology

    Article Title: High-throughput metal susceptibility testing of microbial biofilms

    doi: 10.1186/1471-2180-5-53

    Figure Lengend Snippet: Growth of bacterial biofilms in the MBEC assay . (A) Mean cell density of Pseudomonas aeruginosa ATCC 27853 biofilms on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.842 using one-way ANOVA). (B) SEM photomicrograph of a P. aeruginosa biofilm on the peg surface. (C) Mean cell density of Escherichia coli TG1 on the pegs in different rows of the MBEC assay. Each value is expressed as the mean and standard deviation of 4 to 6 trials. There is no significant difference between cell density of biofilms in the different rows ( p = 0.274 using one-way ANOVA). (D) SEM photomicrograph of an E. coli biofilm on the peg surface. The bar represents 5 μm.

    Article Snippet: In general, biofilms formed using a trough have a 5- to 10-fold greater cell density than those formed using the microtiter plate format (J.J. Harrison, H. Ceri and C. Stremick, unpublished data).

    Techniques: Standard Deviation

    The S-layer and type IV pili are required for biofilm formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.

    Journal: Applied and Environmental Microbiology

    Article Title: Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures

    doi: 10.1128/AEM.02192-18

    Figure Lengend Snippet: The S-layer and type IV pili are required for biofilm formation by Synechocystis . The “attached” data series shows crystal violet binding measured at the OD 600 . The “suspended” data series shows planktonic growth measured at OD 730 . Wza, SD517; Slyr, SD523; PilC, SD519; WT, SD100. Both data series are shown on the same y axis. Error bar corresponds to one standard deviation from the sample mean.

    Article Snippet: Three milliliters of culture was added to each well of a 12-well plate (Corning Costar, catalog no. 07–200–82; Fisher Scientific) that contained a 22-mm-thick glass coverslip as a biofilm substratum (12–540–B; Fisher Scientific).

    Techniques: Binding Assay, Standard Deviation

    Biofouling of a nonaxenic rooftop photobioreactor during growth of WT Synechocystis . (A) During lag phase, no biofilm growth was evident. (B to G) Images taken every 24 h during rapid growth (approximate doubling every 24 h over a period of 5 days). Biofouling such as in the representative images shown was correlated with using hard tap water to prepare BG11 medium; no biofouling was evident when softened tap water was used. Scale bar, ~2 cm. The glass PBR tubes are ~20 cm in diameter.

    Journal: Applied and Environmental Microbiology

    Article Title: Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures

    doi: 10.1128/AEM.02192-18

    Figure Lengend Snippet: Biofouling of a nonaxenic rooftop photobioreactor during growth of WT Synechocystis . (A) During lag phase, no biofilm growth was evident. (B to G) Images taken every 24 h during rapid growth (approximate doubling every 24 h over a period of 5 days). Biofouling such as in the representative images shown was correlated with using hard tap water to prepare BG11 medium; no biofouling was evident when softened tap water was used. Scale bar, ~2 cm. The glass PBR tubes are ~20 cm in diameter.

    Article Snippet: Three milliliters of culture was added to each well of a 12-well plate (Corning Costar, catalog no. 07–200–82; Fisher Scientific) that contained a 22-mm-thick glass coverslip as a biofilm substratum (12–540–B; Fisher Scientific).

    Techniques:

    Percentage biofilm formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).

    Journal: Frontiers in Microbiology

    Article Title: Staphylococcus aureus Quorum Regulator SarA Targeted Compound, 2-[(Methylamino)methyl]phenol Inhibits Biofilm and Down-Regulates Virulence Genes

    doi: 10.3389/fmicb.2017.01290

    Figure Lengend Snippet: Percentage biofilm formed and inhibited in Staphylococcus aureus. (A) Expression levels of SarA in the bacterial strains taken in this study at the log and late phases of growth. (B) Percentage biofilm formation of SarA mutant ALC637 (ΔsarA::795 Tn917LTV1) on treatment and no treatment with 2-[(Methylamino)methyl]phenol by crystal violet method. (C,D) Percentage biofilm inhibition in clinical S. aureus isolates P1966 and AB459 by 2-[(Methylamino)methyl]phenol. All the assays were done in triplicates and the values were expressed as mean ± SD. ∗ Indicates significantly different ( p ≤ 0.05) when compared to untreated (control) with 2-[(Methylamino)methyl]phenol. NS denotes not significant ( P > 0.05).

    Article Snippet: Two and three-dimensional images were captured using a confocal laser scanning microscope with a 40× objective lens to show biofilm distribution (Olympus FLUOVIEW, FV1000).

    Techniques: Expressing, Mutagenesis, Inhibition

    Confocal laser scanning microscopy imaging. Representative images showing the biofilm inhibition effects of 2-[(Methylamino)methyl]phenol at varying concentrations on Staphylococcus aureus P1966 and AB459 during log phase of growth (6 h). The results were in concordance with microtitre plate quantitative assays where biofilm inhibition was more at 1.25 μM. Scale bar in images represents 50 μm.

    Journal: Frontiers in Microbiology

    Article Title: Staphylococcus aureus Quorum Regulator SarA Targeted Compound, 2-[(Methylamino)methyl]phenol Inhibits Biofilm and Down-Regulates Virulence Genes

    doi: 10.3389/fmicb.2017.01290

    Figure Lengend Snippet: Confocal laser scanning microscopy imaging. Representative images showing the biofilm inhibition effects of 2-[(Methylamino)methyl]phenol at varying concentrations on Staphylococcus aureus P1966 and AB459 during log phase of growth (6 h). The results were in concordance with microtitre plate quantitative assays where biofilm inhibition was more at 1.25 μM. Scale bar in images represents 50 μm.

    Article Snippet: Two and three-dimensional images were captured using a confocal laser scanning microscope with a 40× objective lens to show biofilm distribution (Olympus FLUOVIEW, FV1000).

    Techniques: Confocal Laser Scanning Microscopy, Imaging, Inhibition

    Internal architecture of bacterial biofilms on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

    doi: 10.3389/fmicb.2018.00853

    Figure Lengend Snippet: Internal architecture of bacterial biofilms on Aspen roots. 3D-volumes of cell structures were unstacked to deploy a panel of 2D-slices revealing the internal colony architecture. (A) Unstacking of a SBW25 macro-colony highlighting void spaces. One slice every 0.5 μm is shown. (B) Unstacking of a z-directional movie. Maximum intensity and Orthogonal projections from a reconstruction from 60 planes (left) and panel of 2D-slices revealing internal canals.

    Article Snippet: In many Gram-negative bacteria, quorum sensing (QS) plays a pivotal role in biofilm formation through the production and sensing of small diffusible autoinducer (AI) molecules, such as N-Acyl homoserine lactones (AHLs) that monitor cell density and regulate cell behaviors (Newton and Fray, ; Waters and Bassler, ).

    Techniques:

    Phenotype transition network. This network was built from data summarized in Table 2 . In this network, edges (lines with arrows) illustrates an observed transition of one bacterial microscopy phenotype to another. Observed phenotypes were no pattern (NP), long strips (LS), long patches (LP), short patches (SP), high density coating (C), dense biofilms structures (DBS), and filamentous cells (F). “X” represents the final state after 5 weeks, with no o r too few bacteria. Edges are weighted according the frequency of that observation. Nodes are phenotypes, where the size of the node is proportional to the frequency at which that phenotype had been observed.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

    doi: 10.3389/fmicb.2018.00853

    Figure Lengend Snippet: Phenotype transition network. This network was built from data summarized in Table 2 . In this network, edges (lines with arrows) illustrates an observed transition of one bacterial microscopy phenotype to another. Observed phenotypes were no pattern (NP), long strips (LS), long patches (LP), short patches (SP), high density coating (C), dense biofilms structures (DBS), and filamentous cells (F). “X” represents the final state after 5 weeks, with no o r too few bacteria. Edges are weighted according the frequency of that observation. Nodes are phenotypes, where the size of the node is proportional to the frequency at which that phenotype had been observed.

    Article Snippet: In many Gram-negative bacteria, quorum sensing (QS) plays a pivotal role in biofilm formation through the production and sensing of small diffusible autoinducer (AI) molecules, such as N-Acyl homoserine lactones (AHLs) that monitor cell density and regulate cell behaviors (Newton and Fray, ; Waters and Bassler, ).

    Techniques: Microscopy

    Colonization patterns of P. fluorescens strain SBW25 on non-mycorrhizal Aspen roots. Z-stack reconstruction of root surface topology was performed by SDCM at x100 magnification. SBW25 cells are green and plant tissues are visualized using red auto-fluorescence. Scale is indicated by a white bar. Images are representative of colonization patterns on all the observed plant roots. (A) Long strip (LS) colonization pattern observed 1 week after inoculation, (B) long patch (LP) patterns after 2 weeks, (C) short patch (SP) microcolonies formed after 3 weeks, (D,E) bulge–like structures observed along roots after 4-5 weeks, with enlarged images showing dense biofilm-like structures (DBS) in which cells appear encased in a matrix.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

    doi: 10.3389/fmicb.2018.00853

    Figure Lengend Snippet: Colonization patterns of P. fluorescens strain SBW25 on non-mycorrhizal Aspen roots. Z-stack reconstruction of root surface topology was performed by SDCM at x100 magnification. SBW25 cells are green and plant tissues are visualized using red auto-fluorescence. Scale is indicated by a white bar. Images are representative of colonization patterns on all the observed plant roots. (A) Long strip (LS) colonization pattern observed 1 week after inoculation, (B) long patch (LP) patterns after 2 weeks, (C) short patch (SP) microcolonies formed after 3 weeks, (D,E) bulge–like structures observed along roots after 4-5 weeks, with enlarged images showing dense biofilm-like structures (DBS) in which cells appear encased in a matrix.

    Article Snippet: In many Gram-negative bacteria, quorum sensing (QS) plays a pivotal role in biofilm formation through the production and sensing of small diffusible autoinducer (AI) molecules, such as N-Acyl homoserine lactones (AHLs) that monitor cell density and regulate cell behaviors (Newton and Fray, ; Waters and Bassler, ).

    Techniques: Fluorescence, Stripping Membranes

    Persister cells in H. volcanii biofilms. Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p

    Journal: Frontiers in Microbiology

    Article Title: Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii

    doi: 10.3389/fmicb.2017.01589

    Figure Lengend Snippet: Persister cells in H. volcanii biofilms. Comparison of percentage survival of planktonic and biofilm cultures of H. volcanii , following incubation for 6 h in biocidal concentrations of H 2 O 2 , NaClO, and chlorhexidine. Plotted values are the mean of triplicate measurements and error bars represent ± SD. Asterisks denote significance values as determined by paired t -tests: ∗ p

    Article Snippet: Persister Cell Formation in Biofilms Biofilms of H. volcanii were grown using the MBEC device (Innovotech).

    Techniques: Incubation

    Cells at the periphery of the biofilm respond to tobramycin

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Cells at the periphery of the biofilm respond to tobramycin

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Ability of the biofilm to limit penetration can be overcome with high concentrations of tobramycin

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Ability of the biofilm to limit penetration can be overcome with high concentrations of tobramycin

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Metal cations facilitate the penetration of tobramycin into biofilms

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Metal cations facilitate the penetration of tobramycin into biofilms

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Limiting penetration of tobramycin protects biofilm cells

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Limiting penetration of tobramycin protects biofilm cells

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Biofilms limit the penetration of tobramycin into the biomass

    Journal: Environmental microbiology

    Article Title: The extracellular matrix protects Pseudomonas aeruginosa biofilms by limiting the penetration of tobramycin

    doi: 10.1111/1462-2920.12155

    Figure Lengend Snippet: Biofilms limit the penetration of tobramycin into the biomass

    Article Snippet: Biofilms were cultivated in the Calgary Biofilm Device (MBEC™ Physiology and Genetics Assay, Innovotech Inc.) as described previously ( ; ).

    Techniques:

    Quantification of biofilm formation by the wild-type strain (ATCC 17978), a stable knockout mutant strain lacking the gene A1S_0114 (ATCC Δ0114), the same mutant strain containing the pET-RA plasmid (ATCC Δ0114 + PETRA), and a mutant strain containing the pET-RA plasmid harboring the A1S_0114 gene (ATCC Δ0114 + PETRA + 0114).

    Journal: PLoS ONE

    Article Title: Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

    doi: 10.1371/journal.pone.0072968

    Figure Lengend Snippet: Quantification of biofilm formation by the wild-type strain (ATCC 17978), a stable knockout mutant strain lacking the gene A1S_0114 (ATCC Δ0114), the same mutant strain containing the pET-RA plasmid (ATCC Δ0114 + PETRA), and a mutant strain containing the pET-RA plasmid harboring the A1S_0114 gene (ATCC Δ0114 + PETRA + 0114).

    Article Snippet: The complete mRNA transcriptomic profiles of exponentially growing and stationary-phases cultures and from biofilm cells were obtained by Illumina procedures.

    Techniques: Knock-Out, Mutagenesis, Positron Emission Tomography, Plasmid Preparation

    Sequence distribution of the 1621 genes identified in the present work as up-regulated in biofilm vs. stationary phase cells. Genes involved in: A) biological processes, B) cellular components, and C) molecular functions. The results were filtered by the number of sequences (cutoff = 40, 5, and 80, respectively).

    Journal: PLoS ONE

    Article Title: Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

    doi: 10.1371/journal.pone.0072968

    Figure Lengend Snippet: Sequence distribution of the 1621 genes identified in the present work as up-regulated in biofilm vs. stationary phase cells. Genes involved in: A) biological processes, B) cellular components, and C) molecular functions. The results were filtered by the number of sequences (cutoff = 40, 5, and 80, respectively).

    Article Snippet: The complete mRNA transcriptomic profiles of exponentially growing and stationary-phases cultures and from biofilm cells were obtained by Illumina procedures.

    Techniques: Sequencing

    Sequence distribution of genes expressed only in biofilm-associated cells and inhibited in planktonic cells. Genes involved in A) biological processes, B) molecular functions, and C) cellular components. The results were filtered by the number of sequences (cutoff = 1, 4, and 1, respectively).

    Journal: PLoS ONE

    Article Title: Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

    doi: 10.1371/journal.pone.0072968

    Figure Lengend Snippet: Sequence distribution of genes expressed only in biofilm-associated cells and inhibited in planktonic cells. Genes involved in A) biological processes, B) molecular functions, and C) cellular components. The results were filtered by the number of sequences (cutoff = 1, 4, and 1, respectively).

    Article Snippet: The complete mRNA transcriptomic profiles of exponentially growing and stationary-phases cultures and from biofilm cells were obtained by Illumina procedures.

    Techniques: Sequencing

    Quantification of biofilm formation by the wild-type strain (ATCC 17978) and strains with chromosomal disruptions in the genes A1S_0114, A1S_0302, A1S_1507, A1S_3168 and A1S_2042.

    Journal: PLoS ONE

    Article Title: Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells

    doi: 10.1371/journal.pone.0072968

    Figure Lengend Snippet: Quantification of biofilm formation by the wild-type strain (ATCC 17978) and strains with chromosomal disruptions in the genes A1S_0114, A1S_0302, A1S_1507, A1S_3168 and A1S_2042.

    Article Snippet: The complete mRNA transcriptomic profiles of exponentially growing and stationary-phases cultures and from biofilm cells were obtained by Illumina procedures.

    Techniques:

    Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old biofilms ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: Viable counts of each bacterial species present in the initial inoculum (per well) and in the 3‐day old biofilms ( n = 7). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = Aggregatibacter actinomycetemcomitans . Error bars: standard error

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques:

    CLSM images of 3‐day old biofilm after antibiotic exposure. Overlapping of images collected from green and red channel. (a) 3‐day‐old biofilm (negative control); (b) 3‐day old biofilm CHX‐treated for 2 hr; (c) 3‐day old biofilm treated with AMX + MET in high concentration for 2 hr; (d) 3‐day old biofilm treated with PV + MET in high concentration for 2 hr. Z‐stacks were taken in xyz projection with 63× objective, oil immersion, at 10 μm from the biofilm bottom. Scale bar: 10 μm

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: CLSM images of 3‐day old biofilm after antibiotic exposure. Overlapping of images collected from green and red channel. (a) 3‐day‐old biofilm (negative control); (b) 3‐day old biofilm CHX‐treated for 2 hr; (c) 3‐day old biofilm treated with AMX + MET in high concentration for 2 hr; (d) 3‐day old biofilm treated with PV + MET in high concentration for 2 hr. Z‐stacks were taken in xyz projection with 63× objective, oil immersion, at 10 μm from the biofilm bottom. Scale bar: 10 μm

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Confocal Laser Scanning Microscopy, Negative Control, Concentration Assay

    Viable counts of each bacterial species in the 3‐day old biofilms (negative controls) and subjected to antiseptic or antibiotic treatment ( n = 6). No live CFU were retrieved from biofilms treated with CHX (positive controls). Single green bars: number of live Aggregatibacter actinomycetemcomitans retrieved from biofilms exposed to antibiotic combinations in high (H) or low (L) concentrations. * shows statistical significance between biofilms exposed to PV + MET in high and low concentration ( p = .041, t test). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = A . actinomycetemcomitans . Error bars: standard error

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: Viable counts of each bacterial species in the 3‐day old biofilms (negative controls) and subjected to antiseptic or antibiotic treatment ( n = 6). No live CFU were retrieved from biofilms treated with CHX (positive controls). Single green bars: number of live Aggregatibacter actinomycetemcomitans retrieved from biofilms exposed to antibiotic combinations in high (H) or low (L) concentrations. * shows statistical significance between biofilms exposed to PV + MET in high and low concentration ( p = .041, t test). Fn = Fusobacterium nucleatum ; Pg = Porphyromonas gingivalis ; Aa = A . actinomycetemcomitans . Error bars: standard error

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Concentration Assay

    CLSM image in maximum projection of the series taken in xzy axis of the 3‐day old biofilm. Viable and nonviable bacterial cells are depicted in green and red, respectively. Scale bar: 10 μm

    Journal: Clinical and Experimental Dental Research

    Article Title: The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model. The effect of metronidazole plus amoxicillin or metronidazole plus penicillin V on periodontal pathogens in an in vitro biofilm model

    doi: 10.1002/cre2.96

    Figure Lengend Snippet: CLSM image in maximum projection of the series taken in xzy axis of the 3‐day old biofilm. Viable and nonviable bacterial cells are depicted in green and red, respectively. Scale bar: 10 μm

    Article Snippet: 2.2 Biofilm construction Biofilms were prepared in 24‐well plates (Corning Inc., NY, USA) by adapting a previously described protocol (Sanchez et al., ).

    Techniques: Confocal Laser Scanning Microscopy

    Effect of farnesol on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to farnesol at 37.5 μM. (c) Biofilm exposed to farnesol at 150 μM. Concanavalin A-Alexa Fluor 647 conjugate (green stain highlighting the Candida cell

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: Effect of farnesol on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to farnesol at 37.5 μM. (c) Biofilm exposed to farnesol at 150 μM. Concanavalin A-Alexa Fluor 647 conjugate (green stain highlighting the Candida cell

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: Staining

    In vitro interaction between farnesol (0.586–300 μM) and micafungin (0.03–2 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and micafungin (0.03–2 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    Effect of farnesol combination treatment on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to fluconazole at 64 mg/L. (c) Biofilm exposed to combination treatment of farnesol at 37.5 μM plus fluconazole at 64 mg/L. (d) Biofilm

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: Effect of farnesol combination treatment on C. albicans biofilms. (a) Untreated biofilm. (b) Biofilm exposed to fluconazole at 64 mg/L. (c) Biofilm exposed to combination treatment of farnesol at 37.5 μM plus fluconazole at 64 mg/L. (d) Biofilm

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques:

    In vitro interaction between farnesol (0.586–300 μM) and fluconazole (8–512 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and fluconazole (8–512 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    In vitro interaction between farnesol (0.586–300 μM) and amphotericin B (0.5–32 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Journal: Journal of Antimicrobial Chemotherapy

    Article Title: In vitro interactions between farnesol and fluconazole, amphotericin B or micafungin against Candida albicans biofilms

    doi: 10.1093/jac/dku374

    Figure Lengend Snippet: In vitro interaction between farnesol (0.586–300 μM) and amphotericin B (0.5–32 mg/L) against C. albicans biofilms based on the Bliss independence no interaction model. The x -axis and y -axis represent the concentrations of farnesol

    Article Snippet: Biofilms were grown in vitro on the surface of polystyrene, flat-bottom 96-well microtitre plates (Corning Inc., Corning, NY, USA) as previously described.

    Techniques: In Vitro

    Confocal Laser Scanning Microscopy of biofilm formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static biofilms were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Confocal Laser Scanning Microscopy of biofilm formed by S. pseudintermedius strain DSM 25713. Biofilm was allowed to form for 48 h at 37 °C, in absence of serum, under both ( a ) static, and ( b ) dynamic (flow cell chamber) conditions. Static biofilms were further treated for 24 h with increasing gentamicin concentrations (1x-128xMIC). Representative images of biofilm exposed at ( c ) 1x and ( d ) 128xMIC gentamicin are shown. Orthogonal images z are projections of x and y planes, collected within the biofilm as indicated by the green and red lines in the top view. Image capture was set for simultaneous visualization of red (Propidium iodide-stained dead cells), green (Syto-9-stained viable cells), and blue (Concanavalin A-stained EPS) fluorescence. Magnification, x100

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Confocal Laser Scanning Microscopy, Flow Cytometry, Staining, Fluorescence

    Kinetic of biofilm formation, through 72 h-incubation, by S. pseudintermedius strain DSM 25713 onto polystyrene. ( a - f ) Representative SEM images of biofilm formation after 1, 4, 8, 24, 48, and 72 h of incubation, respectively. Magnification (x1.000). ( g , h ) Magnification (x20.000) of ( e ) and ( f ), respectively. Cocci are surrounded by EPS appearing as an extensive network of filaments stretched among cells and between these and the substratum. ( i ) Kinetic of biofilm formation as assessed by viable count. Maximum, median, and minimum values are shown in each box (n = 6)

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Kinetic of biofilm formation, through 72 h-incubation, by S. pseudintermedius strain DSM 25713 onto polystyrene. ( a - f ) Representative SEM images of biofilm formation after 1, 4, 8, 24, 48, and 72 h of incubation, respectively. Magnification (x1.000). ( g , h ) Magnification (x20.000) of ( e ) and ( f ), respectively. Cocci are surrounded by EPS appearing as an extensive network of filaments stretched among cells and between these and the substratum. ( i ) Kinetic of biofilm formation as assessed by viable count. Maximum, median, and minimum values are shown in each box (n = 6)

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation

    ESEM images of biofilm formed by S. pseudintermedius strain DSM 25713 onto polystyrene following 72 h-incubation. ( a ) Biofilm exhibited spatially heterogeneous organization, as suggested by the presence of “mushroom-like” structures (as indicated by arrows). Magnification: x3.000. ( b , c ) Multilayered organization with the presence of bacteria under EPS matrix (as indicated by arrows). Magnification: x12.500 and x20.000, respectively

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: ESEM images of biofilm formed by S. pseudintermedius strain DSM 25713 onto polystyrene following 72 h-incubation. ( a ) Biofilm exhibited spatially heterogeneous organization, as suggested by the presence of “mushroom-like” structures (as indicated by arrows). Magnification: x3.000. ( b , c ) Multilayered organization with the presence of bacteria under EPS matrix (as indicated by arrows). Magnification: x12.500 and x20.000, respectively

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation

    Standardization of experimental conditions for biofilm formation by S. pseudintermedius strain DSM 25713 on polystyrene surface. Effect of dynamic (filled squares) or static (filled triangles) incubation, incubation time (24, 48, and 72 h), and inoculum concentration (10 5 , 10 6 , and 10 7 CFU/mL) on biofilm biomass formation, as assessed by spectrophotometric assay. Values are means ± SDs (n = 6). *** p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Standardization of experimental conditions for biofilm formation by S. pseudintermedius strain DSM 25713 on polystyrene surface. Effect of dynamic (filled squares) or static (filled triangles) incubation, incubation time (24, 48, and 72 h), and inoculum concentration (10 5 , 10 6 , and 10 7 CFU/mL) on biofilm biomass formation, as assessed by spectrophotometric assay. Values are means ± SDs (n = 6). *** p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Incubation, Concentration Assay, Spectrophotometric Assay

    Effect of serum and pH on biofilm formation and growth by S. pseudintermedius strain DSM 25713. ( a ) Serum was tested against biofilm formation at various dilutions (1:2, 1:10, and 1:100), as free or adsorbed to polystyrene, under different pH (5.5, 7.1, and 8.7). Control wells contained bacteria but not serum. Biofilm biomass amount was measured by crystal violet assay, then normalized on bacterial growth by calculating the specific biofilm formation (SBF) index (see Materials and Methods). ( b ) The effect of free serum against bacterial growth was assessed by measuring OD 600 of cell grown in broth following 24 h-incubation. Results are means + SDs (n = 9). * p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: Effect of serum and pH on biofilm formation and growth by S. pseudintermedius strain DSM 25713. ( a ) Serum was tested against biofilm formation at various dilutions (1:2, 1:10, and 1:100), as free or adsorbed to polystyrene, under different pH (5.5, 7.1, and 8.7). Control wells contained bacteria but not serum. Biofilm biomass amount was measured by crystal violet assay, then normalized on bacterial growth by calculating the specific biofilm formation (SBF) index (see Materials and Methods). ( b ) The effect of free serum against bacterial growth was assessed by measuring OD 600 of cell grown in broth following 24 h-incubation. Results are means + SDs (n = 9). * p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: Crystal Violet Assay, Incubation

    In vitro effect of antibiotics against preformed biofilm by S. pseudintermedius strain DSM 25713. Biofilms allowed to form following 48 h-incubation were exposed for further 24 h to each antibiotic at concentrations equal or multiple of MIC. Results are expressed as percentage of biofilm’s viability – as assessed by viable colony count - compared to control (unexposed, 100 % viability) (n = 6). The dotted line indicates a reduction in biofilm viability of at least 20 % vs control ( p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: In vitro effect of antibiotics against preformed biofilm by S. pseudintermedius strain DSM 25713. Biofilms allowed to form following 48 h-incubation were exposed for further 24 h to each antibiotic at concentrations equal or multiple of MIC. Results are expressed as percentage of biofilm’s viability – as assessed by viable colony count - compared to control (unexposed, 100 % viability) (n = 6). The dotted line indicates a reduction in biofilm viability of at least 20 % vs control ( p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: In Vitro, Incubation

    In vitro activity of antibiotics at sub-inhibitory concentrations against biofilm formation by S. pseudintermedius strain DSM 25713. Biofilm biomass formed during 24 h-incubation was measured, using the crystal violet assay, in the presence of antibiotics at concentrations equal to 1/2x, 1/4x, and 1/8xMIC. Results were plotted as percentage of biofilm biomass formed in the presence of antibiotic, compared to controls (not exposed, 100 % biofilm biomass) (n = 6). The dotted line indicates a reduction in biofilm biomass of at least 20 % vs control ( p

    Journal: BMC Microbiology

    Article Title: New insights in Staphylococcus pseudintermedius pathogenicity: antibiotic-resistant biofilm formation by a human wound-associated strain

    doi: 10.1186/s12866-015-0449-x

    Figure Lengend Snippet: In vitro activity of antibiotics at sub-inhibitory concentrations against biofilm formation by S. pseudintermedius strain DSM 25713. Biofilm biomass formed during 24 h-incubation was measured, using the crystal violet assay, in the presence of antibiotics at concentrations equal to 1/2x, 1/4x, and 1/8xMIC. Results were plotted as percentage of biofilm biomass formed in the presence of antibiotic, compared to controls (not exposed, 100 % biofilm biomass) (n = 6). The dotted line indicates a reduction in biofilm biomass of at least 20 % vs control ( p

    Article Snippet: Time course of biofilm formation Biofilms were allowed to form in each well of a 24-well flat-bottom polystyrene tissue-treated microtiter plate (BD Company), as described above.

    Techniques: In Vitro, Activity Assay, Incubation, Crystal Violet Assay

    Antimicrobial activity of ColA-43864-His8. Effect of IMAC-purified ColA-43864 on planktonic ( a ) or biofilm ( b ) planktonic bacteria. C. freundii NCTC 9750 (6 × 10 9 and 2 × 10 6 CFU ml −1 for planktonic and biofilm, respectively) were incubated, for 30 min, in the presence of 2–0.02 μg IMAC-purified ColA-43864, PBS control and mock IMAC-purified sample from E. coli S17-pMQ124. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation

    Journal: Archives of microbiology

    Article Title: Isolation and identification of a bacteriocin with antibacterial and antibiofilm activity from Citrobacter freundii

    doi: 10.1007/s00203-012-0793-2

    Figure Lengend Snippet: Antimicrobial activity of ColA-43864-His8. Effect of IMAC-purified ColA-43864 on planktonic ( a ) or biofilm ( b ) planktonic bacteria. C. freundii NCTC 9750 (6 × 10 9 and 2 × 10 6 CFU ml −1 for planktonic and biofilm, respectively) were incubated, for 30 min, in the presence of 2–0.02 μg IMAC-purified ColA-43864, PBS control and mock IMAC-purified sample from E. coli S17-pMQ124. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation

    Article Snippet: Biofilms were formed in a non-tissue culture treated, 96-well polyvinyl chloride microtiter dishes (Becton–Dickinson, Franklin Lakes, NJ, USA) as previously described ( ; ).

    Techniques: Activity Assay, Purification, Incubation, Standard Deviation

    Antimicrobial activity of crude ColA-43864 extract. a Effect of ColA-43864 on planktonic bacteria. Tested bacteria (~10 9 CFU ml −1 ) were incubated for 30 min with PBS ( black bars ), 87 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ), and 37 μg protein isolated from E. coli S17-pMQ348 ( gray bars ). Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. b Effect of ColA-43864 on biofilms. Overnight biofilms (composed of ~10 6 –10 7 CFU ml −1 ) were incubated for 120 min with PBS ( black bars ) and 175 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ). Biofilms were also incubated, for 30 min ( gray bars ) and 120 min ( striped gray bars ), with 75 μg protein isolated from E. coli S17-pMQ348. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. c CLSM micrographs demonstrating the effect of ColA-43864 on biofilms. Overnight biofilms of C. freundii ATCC 8090 were incubated for 60 min with protein (11.6 μg ml −1 final concentration) extracted from empty vector control E. coli S17-pMQ124 or the colicin bearing plasmid E. coli S17-pMQ348. Thereafter, the biofilms were stained with Syto-9 (live) and propidium iodide (dead). A representative image is shown. Images were taken at the same exposures with a 40× magnification objective

    Journal: Archives of microbiology

    Article Title: Isolation and identification of a bacteriocin with antibacterial and antibiofilm activity from Citrobacter freundii

    doi: 10.1007/s00203-012-0793-2

    Figure Lengend Snippet: Antimicrobial activity of crude ColA-43864 extract. a Effect of ColA-43864 on planktonic bacteria. Tested bacteria (~10 9 CFU ml −1 ) were incubated for 30 min with PBS ( black bars ), 87 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ), and 37 μg protein isolated from E. coli S17-pMQ348 ( gray bars ). Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. b Effect of ColA-43864 on biofilms. Overnight biofilms (composed of ~10 6 –10 7 CFU ml −1 ) were incubated for 120 min with PBS ( black bars ) and 175 μg protein extracted from empty vector control E. coli S17-pMQ124 ( white bars ). Biofilms were also incubated, for 30 min ( gray bars ) and 120 min ( striped gray bars ), with 75 μg protein isolated from E. coli S17-pMQ348. Cell viability was measured at time 0 and following incubation. Each value represents the mean of 3 experiments. Error bars are shown as one-standard deviation. c CLSM micrographs demonstrating the effect of ColA-43864 on biofilms. Overnight biofilms of C. freundii ATCC 8090 were incubated for 60 min with protein (11.6 μg ml −1 final concentration) extracted from empty vector control E. coli S17-pMQ124 or the colicin bearing plasmid E. coli S17-pMQ348. Thereafter, the biofilms were stained with Syto-9 (live) and propidium iodide (dead). A representative image is shown. Images were taken at the same exposures with a 40× magnification objective

    Article Snippet: Biofilms were formed in a non-tissue culture treated, 96-well polyvinyl chloride microtiter dishes (Becton–Dickinson, Franklin Lakes, NJ, USA) as previously described ( ; ).

    Techniques: Activity Assay, Incubation, Plasmid Preparation, Isolation, Standard Deviation, Confocal Laser Scanning Microscopy, Concentration Assay, Staining

    Biofilm formation by Acinetobacter. Biofilm formation after 24 h at 28°C for the clinically relevant A. baumannii (n = 45), A. gen. sp. 3 (n = 3) and A. gen. sp. 13TU (n = 3) and for the clinically less-relevant A. calcoaceticus (n = 3) and A. junii (n = 7). Data are expressed as mean biofilm mass (in arbitrary units (a.u.)) of three independent experiments; each performed in sixplicate. Outbreak-associated (+) or non-outbreak-associated (−) isolate. European clone I (I), II (II) or III (III) isolate. Multidrug resistant (MDR; +) or susceptible (−) isolate.

    Journal: PLoS ONE

    Article Title: Do Biofilm Formation and Interactions with Human Cells Explain the Clinical Success of Acinetobacter baumannii?

    doi: 10.1371/journal.pone.0010732

    Figure Lengend Snippet: Biofilm formation by Acinetobacter. Biofilm formation after 24 h at 28°C for the clinically relevant A. baumannii (n = 45), A. gen. sp. 3 (n = 3) and A. gen. sp. 13TU (n = 3) and for the clinically less-relevant A. calcoaceticus (n = 3) and A. junii (n = 7). Data are expressed as mean biofilm mass (in arbitrary units (a.u.)) of three independent experiments; each performed in sixplicate. Outbreak-associated (+) or non-outbreak-associated (−) isolate. European clone I (I), II (II) or III (III) isolate. Multidrug resistant (MDR; +) or susceptible (−) isolate.

    Article Snippet: Biofilm formation Biofilm formation in 96-wells polyvinylchloride microtiter plates (Falcon, BD, Breda, the Netherlands) was assayed as described .

    Techniques:

    Liposomal clarithromycin activity on P. aureginosa PA-13572 biofilm (MBEC assay). Free (F-CAM) or liposomal formulations were introduced to mature biofilm at concentrations of 32 mg/liter (a), 64 mg/liter (b), and 128 mg/liter (c). Untreated biofilm acted as a control. The data represent three independent experiments in triplicate and are shown as means ± SEM. P values were considered significant compared with the control: ***, P

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Efficacy and Safety of Liposomal Clarithromycin and Its Effect on Pseudomonas aeruginosa Virulence Factors

    doi: 10.1128/AAC.00235-13

    Figure Lengend Snippet: Liposomal clarithromycin activity on P. aureginosa PA-13572 biofilm (MBEC assay). Free (F-CAM) or liposomal formulations were introduced to mature biofilm at concentrations of 32 mg/liter (a), 64 mg/liter (b), and 128 mg/liter (c). Untreated biofilm acted as a control. The data represent three independent experiments in triplicate and are shown as means ± SEM. P values were considered significant compared with the control: ***, P

    Article Snippet: In order to assess the minimum biofilm eradication concentration (MBEC), P. aeruginosa strain PA-13572 was allowed to form a biofilm in a Calgary biofilm plate (Innovotech, Edmonton, AB, Canada) as previously reported ( ).

    Techniques: Activity Assay, Chick Chorioallantoic Membrane Assay

    Tracking and quantification of biofilm community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Tracking and quantification of biofilm community structure changes after temperature increase. ( a ) viSNE submaps ( Fig. 2a ) belonging to days 0, 7, 14 and 21 post temperature increase. More colour-intense regions of the submaps depict regions of higher cell density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, five independent microcosms) and time points indicated that the detected changes in community structure were governed by time point and not biological or technical noise ( Supplementary Fig. 10 ). ( b ) Quantification of subpopulations defined in Fig. 2b , pooled from five biological replicates for each time point after temperature increase (all biological replicates are depicted in Supplementary Fig. 11 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 9 .

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques:

    Categorizing subpopulations in temperature-stressed stream biofilms. ( a ) Stream biofilms were assessed by FC directly after transfer to higher temperature, after 1, 2 and 3 weeks and the acquired data was altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell from the biofilms, or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set of wavelengths displayed in Supplementary Fig. 6 ). ( b ) Subpopulations (LA1–LA15) categorized based on the viSNE map, optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 6 ). A fraction of the particles (4.5–5.8%) was not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples allowed for assigning subpopulations to types of organisms and potentially decaying cells ( Supplementary Fig. 8 ).

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Categorizing subpopulations in temperature-stressed stream biofilms. ( a ) Stream biofilms were assessed by FC directly after transfer to higher temperature, after 1, 2 and 3 weeks and the acquired data was altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell from the biofilms, or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set of wavelengths displayed in Supplementary Fig. 6 ). ( b ) Subpopulations (LA1–LA15) categorized based on the viSNE map, optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 6 ). A fraction of the particles (4.5–5.8%) was not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples allowed for assigning subpopulations to types of organisms and potentially decaying cells ( Supplementary Fig. 8 ).

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Fluorescence

    Tracking biofilm community structure changes along a stream. ( a ) viSNE submaps belonging to six sites (A–F) along the stream Mönchaltorfer Aa. More colour-intense regions of the submaps depict regions of higher cell or particle density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, 3 stones per site) and sites indicated that the detected changes in community structure were governed by site and not biological or technical noise ( Supplementary Fig. 17 ). The sites are characterized in Supplementary Tables 4–6 . Site A is at the spring of the stream in the forest, site B is in an unshaded stretch, site C is shaded but in the straightened section of the stream-like sites D–F, which are additionally influenced by waste-water treatment plant effluents, site D being situated immediately downstream a treatment plant. ( b ) Subpopulations are defined in Fig. 4b , pooled from three biological replicates taken from each site (all biological replicates are depicted in Supplementary Fig. 18 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 16 . ( c ) Biplots of the redundancy analysis (RDA) based on the fraction of cells/particles in the subpopulations in Fig. 4b constrained by forward selected field physico-chemical parameters ( Supplementary Tables 4,6 ). Dots/grey tones: specific sampling sites. Dispersion of standard error of the weighted scores of sampling sites are shown as ellipses in the respective grey tone (confidence limit=0.95). Centroids of the subpopulations (MA1a–MA10) are given. Significantly tested model variables are depicted (*** P

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Tracking biofilm community structure changes along a stream. ( a ) viSNE submaps belonging to six sites (A–F) along the stream Mönchaltorfer Aa. More colour-intense regions of the submaps depict regions of higher cell or particle density. Similarity analysis of technical replicates (that is, three per sample), biological replicates (that is, 3 stones per site) and sites indicated that the detected changes in community structure were governed by site and not biological or technical noise ( Supplementary Fig. 17 ). The sites are characterized in Supplementary Tables 4–6 . Site A is at the spring of the stream in the forest, site B is in an unshaded stretch, site C is shaded but in the straightened section of the stream-like sites D–F, which are additionally influenced by waste-water treatment plant effluents, site D being situated immediately downstream a treatment plant. ( b ) Subpopulations are defined in Fig. 4b , pooled from three biological replicates taken from each site (all biological replicates are depicted in Supplementary Fig. 18 ). Statistical analysis of subpopulation sizes is available in Supplementary Fig. 16 . ( c ) Biplots of the redundancy analysis (RDA) based on the fraction of cells/particles in the subpopulations in Fig. 4b constrained by forward selected field physico-chemical parameters ( Supplementary Tables 4,6 ). Dots/grey tones: specific sampling sites. Dispersion of standard error of the weighted scores of sampling sites are shown as ellipses in the respective grey tone (confidence limit=0.95). Centroids of the subpopulations (MA1a–MA10) are given. Significantly tested model variables are depicted (*** P

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Sampling

    Categorizing subpopulations in stream biofilms sampled in the field. ( a ) Stream biofilms were assessed by FC after sampling at six sites along the stream Mönchaltorfer Aa and altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell or particle from the biofilms or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set displayed in Supplementary Fig. 13 ). ( b ) Subpopulations (MA 1–10) categorized based on the viSNE map and optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 13 ). Some cells (range 2.7–11.2 %) were not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples ( Supplementary Fig. 15 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Categorizing subpopulations in stream biofilms sampled in the field. ( a ) Stream biofilms were assessed by FC after sampling at six sites along the stream Mönchaltorfer Aa and altogether mapped by viSNE. viSNE maps are shown in single colour, with each point in the viSNE map representing a single cell or particle from the biofilms or coloured according to FS and fluorescence intensity at specific wavelengths (nm) measured by FC (full set displayed in Supplementary Fig. 13 ). ( b ) Subpopulations (MA 1–10) categorized based on the viSNE map and optical scatter and fluorescence intensities ( a ) ( Supplementary Fig. 13 ). Some cells (range 2.7–11.2 %) were not categorized due to lack of distinct properties. Comparison of subpopulation properties with data acquired from reference species and pigment-bleached reference samples ( Supplementary Fig. 15 ) allowed for assigning subpopulations to types of organisms and potentially decaying cells.

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Sampling, Fluorescence

    Detection of microplastics in stream biofilms. ( a ) viSNE map shown in Fig. 4a with circled hypothetical microplastic cluster. ( b ) SEM image of a potential microplastic particle isolated from site D. Scale bar, 10 μm. ( c ) SEM image of polystyrene beads isolated from a spiked sample. Scale bar, 50 μm. The squares in the top right corner of the SEM images ( b , c ) with separate scale bars, 1 μm, depict the region scanned for EDS analysis. ( d ) EDS spectrum of a potential microplastic particle isolated from site D. ( e ) EDS spectrum of polystyrene beads isolated from a spiked sample.

    Journal: Nature Communications

    Article Title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

    doi: 10.1038/ncomms11587

    Figure Lengend Snippet: Detection of microplastics in stream biofilms. ( a ) viSNE map shown in Fig. 4a with circled hypothetical microplastic cluster. ( b ) SEM image of a potential microplastic particle isolated from site D. Scale bar, 10 μm. ( c ) SEM image of polystyrene beads isolated from a spiked sample. Scale bar, 50 μm. The squares in the top right corner of the SEM images ( b , c ) with separate scale bars, 1 μm, depict the region scanned for EDS analysis. ( d ) EDS spectrum of a potential microplastic particle isolated from site D. ( e ) EDS spectrum of polystyrene beads isolated from a spiked sample.

    Article Snippet: Sample preparation and FC Suspensions of reference species and biofilms grown indoors or sampled in the field were sonicated (45 kHz 60 W, VWR Ultrasonic Cleaner) for 1 min to break up colonies, filtered through 50 μm filters (Partec) and immediately fixed (0.01% paraformaldehyde and 0.1% glutaraldehyde (w/v, stock in tap water)) at 4 °C overnight.

    Techniques: Isolation

    Antibiofilm activity of bacteriocin on S. epidermidis biofilm formation as well as eradication of established biofilm at different concentrations detected by crystal violet staining assay.

    Journal: Medical Principles and Practice

    Article Title: Antibacterial Activity, Cytotoxicity, and the Mechanism of Action of Bacteriocin from Bacillus subtilis GAS101

    doi: 10.1159/000487306

    Figure Lengend Snippet: Antibiofilm activity of bacteriocin on S. epidermidis biofilm formation as well as eradication of established biofilm at different concentrations detected by crystal violet staining assay.

    Article Snippet: The adhered cells of biofilm were stained with crystal violet (CV) dye as described by Sharma et al. [ ], and the absorbance of the plate was measured at 595 nm in an ELISA reader (BioRad, CA, USA).

    Techniques: Activity Assay, Staining

    CiaRH is required for biofilm formation by the ΔsdbA mutant. (a) Crystal violet staining of 24 h biofilms grown in 24-well plates. Biofilms were grown with the parent, ΔsdbA , sdbA -complemented mutant (+SdbA), ΔciaRH , ΔsdbAΔciaRH double mutant, and ΔsdbA ciaRH -complemented mutant ( ΔsdbA + CiaRH). Results are means ± SD of at least three experiments. The lower panel shows representative wells after staining. (b) In parallel to the biofilm formation assay, three additional wells for each strain were tested for total growth. The optical density was measured for the combined biofilm and planktonic cells for each mutant. (c) Biofilm formation of single deletion mutants for ciaRH and degP in the parent strain. Biofilms were grown for 24 h in 24-well plates prior to staining. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the parent (*** P ≤ 0.001, **** P ≤ 0.0001).

    Journal: PLoS ONE

    Article Title: Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System

    doi: 10.1371/journal.pone.0166656

    Figure Lengend Snippet: CiaRH is required for biofilm formation by the ΔsdbA mutant. (a) Crystal violet staining of 24 h biofilms grown in 24-well plates. Biofilms were grown with the parent, ΔsdbA , sdbA -complemented mutant (+SdbA), ΔciaRH , ΔsdbAΔciaRH double mutant, and ΔsdbA ciaRH -complemented mutant ( ΔsdbA + CiaRH). Results are means ± SD of at least three experiments. The lower panel shows representative wells after staining. (b) In parallel to the biofilm formation assay, three additional wells for each strain were tested for total growth. The optical density was measured for the combined biofilm and planktonic cells for each mutant. (c) Biofilm formation of single deletion mutants for ciaRH and degP in the parent strain. Biofilms were grown for 24 h in 24-well plates prior to staining. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the parent (*** P ≤ 0.001, **** P ≤ 0.0001).

    Article Snippet: To test the effect of peptides on biofilm formation, biofilms were prepared as described above except that 0.5 μg of either CSP (DVRSNKIRLWWENIFFNKK; Biomatik, Cambridge, ON, Canada) or a fragment of Sth1 (AGFTGGIAVGLNRVNRK; Biomatik) was added to each well during the initial biofilm setup.

    Techniques: Mutagenesis, Staining, Tube Formation Assay

    Characterization of ΔsdbA biofilms. (a) Alcian blue binding assay for surface charge in cells grown to early stationary phase in HTVG medium (Inoculum), and (b) in cells grown in 24 h biofilms (Biofilm). Bars represent the percentage of unbound dye. (c) Total carbohydrate production. (d) Sensitivity to DNase I and trypsin. Biofilms were grown for 24 h prior to the addition of either DNase I or trypsin, and incubated for an additional 1 h before staining with crystal violet. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the control biofilm for each strain (*** P ≤ 0.001** P

    Journal: PLoS ONE

    Article Title: Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System

    doi: 10.1371/journal.pone.0166656

    Figure Lengend Snippet: Characterization of ΔsdbA biofilms. (a) Alcian blue binding assay for surface charge in cells grown to early stationary phase in HTVG medium (Inoculum), and (b) in cells grown in 24 h biofilms (Biofilm). Bars represent the percentage of unbound dye. (c) Total carbohydrate production. (d) Sensitivity to DNase I and trypsin. Biofilms were grown for 24 h prior to the addition of either DNase I or trypsin, and incubated for an additional 1 h before staining with crystal violet. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the control biofilm for each strain (*** P ≤ 0.001** P

    Article Snippet: To test the effect of peptides on biofilm formation, biofilms were prepared as described above except that 0.5 μg of either CSP (DVRSNKIRLWWENIFFNKK; Biomatik, Cambridge, ON, Canada) or a fragment of Sth1 (AGFTGGIAVGLNRVNRK; Biomatik) was added to each well during the initial biofilm setup.

    Techniques: Binding Assay, Incubation, Staining

    CiaRH expression in the S . gordonii biofilms. Expression of the cia -induced genes ciaR and degP in the biofilm inoculum and in 24 h biofilms. (a) Expression of ciaR in the parent, ΔsdbA mutant, and sdbA -complemented mutant (+SdbA) in the biofilm inoculum. RNA was isolated from cells grown to early stationary phase in HTVG medium. (b) Expression of degP in the biofilm inoculum. Biofilms were grown in a defined biofilm medium (BM), and RNA was isolated from biofilm cells grown in BM medium for 24 h. (c) Expression of ciaR and (d) degP in 24 h biofilms. Results are means ± SD of three experiments. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the parent (** P

    Journal: PLoS ONE

    Article Title: Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System

    doi: 10.1371/journal.pone.0166656

    Figure Lengend Snippet: CiaRH expression in the S . gordonii biofilms. Expression of the cia -induced genes ciaR and degP in the biofilm inoculum and in 24 h biofilms. (a) Expression of ciaR in the parent, ΔsdbA mutant, and sdbA -complemented mutant (+SdbA) in the biofilm inoculum. RNA was isolated from cells grown to early stationary phase in HTVG medium. (b) Expression of degP in the biofilm inoculum. Biofilms were grown in a defined biofilm medium (BM), and RNA was isolated from biofilm cells grown in BM medium for 24 h. (c) Expression of ciaR and (d) degP in 24 h biofilms. Results are means ± SD of three experiments. Data were analyzed by one-way ANOVA and asterisks indicate a significant difference from the parent (** P

    Article Snippet: To test the effect of peptides on biofilm formation, biofilms were prepared as described above except that 0.5 μg of either CSP (DVRSNKIRLWWENIFFNKK; Biomatik, Cambridge, ON, Canada) or a fragment of Sth1 (AGFTGGIAVGLNRVNRK; Biomatik) was added to each well during the initial biofilm setup.

    Techniques: Expressing, Mutagenesis, Isolation

    CSP diminishes biofilm formation by the ΔsdbA mutant. Crystal violet staining of 24 h biofilms grown in the presence of either CSP, Sth 1 bacteriocin (Sth), or without added peptide (Control). Biofilms were grown with the parent, ΔsdbA , sdbA -complemented mutant (+SdbA), ΔciaRH , ΔsdbAΔciaRH double mutant, and ΔsdbA ciaRH -complemented mutant ( ΔsdbA +CiaRH). Results are means ± SD of three experiments. Asterisks indicate a significant difference from the control biofilm for each strain, as determined by one-way ANOVA (**** P

    Journal: PLoS ONE

    Article Title: Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System

    doi: 10.1371/journal.pone.0166656

    Figure Lengend Snippet: CSP diminishes biofilm formation by the ΔsdbA mutant. Crystal violet staining of 24 h biofilms grown in the presence of either CSP, Sth 1 bacteriocin (Sth), or without added peptide (Control). Biofilms were grown with the parent, ΔsdbA , sdbA -complemented mutant (+SdbA), ΔciaRH , ΔsdbAΔciaRH double mutant, and ΔsdbA ciaRH -complemented mutant ( ΔsdbA +CiaRH). Results are means ± SD of three experiments. Asterisks indicate a significant difference from the control biofilm for each strain, as determined by one-way ANOVA (**** P

    Article Snippet: To test the effect of peptides on biofilm formation, biofilms were prepared as described above except that 0.5 μg of either CSP (DVRSNKIRLWWENIFFNKK; Biomatik, Cambridge, ON, Canada) or a fragment of Sth1 (AGFTGGIAVGLNRVNRK; Biomatik) was added to each well during the initial biofilm setup.

    Techniques: Mutagenesis, Staining

    Biofilm production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Biofilm production dynamics after extubation in 9 ETT-MRSA isolates under O 2 or 5% CO 2 Each color-bar represents the biofilm production of each ETT-MRSA isolate compared with the MRSA-in over days 1–8 after extubation. ( A ) Biofilm production dynamics under O 2 . Maximum biofilm production was on day 2. ( B ) Biofilm production dynamics under CO 2 . Maximum biofilm production was on day 1. Since the 5% CO 2 atmosphere better mimics the atmospheric conditions of mechanical ventilation. When ETT-MRSA are rapidly switched from the ETT environment to O 2 alone, they would need a day to adapt their metabolism to the new atmospheric conditions. Black points represent median biofilm production of the 9 isolates each day. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Representative scanning electron microscopy of in vivo MRSA biofilm ( A ) Isolate 1 showing an in vivo detached biofilm at low magnification. Sometimes the sample processing for scanning electron microscopy released the biofilm cluster from the endotracheal tube surface. At higher magnification ( B ), cocci morphologies can be distinguished. The pig from which we obtained Isolate 1 was treated with vancomycin. ( C ) Isolate 45 (from a placebo treated pig) showing an in vivo biofilm attached to the endotracheal tube at low magnification. ( D ) at higher magnification, a cocci biofilm cluster was found (white arrow). Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Representative scanning electron microscopy of in vivo MRSA biofilm ( A ) Isolate 1 showing an in vivo detached biofilm at low magnification. Sometimes the sample processing for scanning electron microscopy released the biofilm cluster from the endotracheal tube surface. At higher magnification ( B ), cocci morphologies can be distinguished. The pig from which we obtained Isolate 1 was treated with vancomycin. ( C ) Isolate 45 (from a placebo treated pig) showing an in vivo biofilm attached to the endotracheal tube at low magnification. ( D ) at higher magnification, a cocci biofilm cluster was found (white arrow). Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques: Electron Microscopy, In Vivo

    Biofilm production of 52 ETT-MRSA isolates compared with the MRSA-in under ambient air or ambient air with 5% CO 2. Each bar represents the biofilm production of each ETT-MRSA isolate versus the MRSA-in (black bar). ( A ) Biofilm production O 2 on day 2 after extubation (peak production); 50% of ETT-MRSA isolates increased biofilm production more than double that of MRSA-in. ( B ) Biofilm production under 5% CO 2 on day 1 after extubation (peak production); 40% of ETT-MRSA isolates increased more than twice MRSA-in biofilm production. The highest biofilm producers ETT-MRSA isolates (n = 9), in dark gray, under both O 2 and 5% CO 2 were selected to undergo the biofilm production dynamics post-extubation. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Biofilm production of 52 ETT-MRSA isolates compared with the MRSA-in under ambient air or ambient air with 5% CO 2. Each bar represents the biofilm production of each ETT-MRSA isolate versus the MRSA-in (black bar). ( A ) Biofilm production O 2 on day 2 after extubation (peak production); 50% of ETT-MRSA isolates increased biofilm production more than double that of MRSA-in. ( B ) Biofilm production under 5% CO 2 on day 1 after extubation (peak production); 40% of ETT-MRSA isolates increased more than twice MRSA-in biofilm production. The highest biofilm producers ETT-MRSA isolates (n = 9), in dark gray, under both O 2 and 5% CO 2 were selected to undergo the biofilm production dynamics post-extubation. Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Representative confocal laser scanning microscopy of in vivo MRSA biofilm Biofilm clusters (white arrows) were stained with the LIVE/DEAD BacLight kit (INVITROGEN, Barcelona, Spain). Viable bacteria (stained green by SYTO 9) are visible, but dead bacteria (stained red by propidium iodide) were infrequently detected. The nuclei and cytoplasm of eukaryotic cells from the pig were also stained nonspecifically by propidium iodide and SYTO 9 (large red and green blotches, respectively). ( A , B ) correspond to the in vivo biofilms of Isolate 39 and Isolate 45 obtained from pigs treated with vancomycin and placebo, respectively. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Representative confocal laser scanning microscopy of in vivo MRSA biofilm Biofilm clusters (white arrows) were stained with the LIVE/DEAD BacLight kit (INVITROGEN, Barcelona, Spain). Viable bacteria (stained green by SYTO 9) are visible, but dead bacteria (stained red by propidium iodide) were infrequently detected. The nuclei and cytoplasm of eukaryotic cells from the pig were also stained nonspecifically by propidium iodide and SYTO 9 (large red and green blotches, respectively). ( A , B ) correspond to the in vivo biofilms of Isolate 39 and Isolate 45 obtained from pigs treated with vancomycin and placebo, respectively. Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques: Confocal Laser Scanning Microscopy, In Vivo, Staining

    Effect of systemic antibiotic treatment on biofilm production in the 52 ETT-MRSA isolates under O 2 or 5% CO 2 conditions Median (interquartile range) values for biofilm production of the 52 ETT-MRSA compared with the MRSA-in under O 2 ( A ) and 5% CO 2 ( B ). Time of assessment: day of peak production. Biofilm production was not influenced by systemic treatment with placebo (n = 19), linezolid (n = 11), or vancomycin (n = 22) under either O 2 (1.96 [0.61–3.02], 2.30 [0.64–3.83], and 1.49 [0.63–2.67], respectively; p = 0.92) or 5% CO 2 (2.02 [1.16–2.34], 1.36 [0.48–2.75], and 1.09 [0.34–2.38], respectively; p = 0.62). Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Journal: Scientific Reports

    Article Title: Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

    doi: 10.1038/s41598-018-30494-7

    Figure Lengend Snippet: Effect of systemic antibiotic treatment on biofilm production in the 52 ETT-MRSA isolates under O 2 or 5% CO 2 conditions Median (interquartile range) values for biofilm production of the 52 ETT-MRSA compared with the MRSA-in under O 2 ( A ) and 5% CO 2 ( B ). Time of assessment: day of peak production. Biofilm production was not influenced by systemic treatment with placebo (n = 19), linezolid (n = 11), or vancomycin (n = 22) under either O 2 (1.96 [0.61–3.02], 2.30 [0.64–3.83], and 1.49 [0.63–2.67], respectively; p = 0.92) or 5% CO 2 (2.02 [1.16–2.34], 1.36 [0.48–2.75], and 1.09 [0.34–2.38], respectively; p = 0.62). Abbreviations: 5% CO 2 , ambient air with 5% CO 2 ; O 2 , ambient air; ETT-MRSA, clinical MRSA isolates from endotracheal tubes; MRSA-in, MRSA inoculated into pigs’ lungs; MRSA, methicillin-resistant Staphylococcus aureus .

    Article Snippet: The optical density of biofilm was measured in a Synergy 2 Multimode Microplate Reader (BIOTEK Instruments, Inc., USA) at a wavelength of 490 nm.

    Techniques:

    Cell density [log 10 (CFU/cm 2 )] of the 1 (black) and 7 (red) day(s) old dual-species biofilm as function of the CAP treatment time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Geeraerd et al. ( 2000 ) model are represented: total population on general medium (□, solid line), L. monocytogenes population on Palcam medium (x, dashed line), and S . Typhimurium population on XLD medium (♢, dotted line).

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Cell density [log 10 (CFU/cm 2 )] of the 1 (black) and 7 (red) day(s) old dual-species biofilm as function of the CAP treatment time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Geeraerd et al. ( 2000 ) model are represented: total population on general medium (□, solid line), L. monocytogenes population on Palcam medium (x, dashed line), and S . Typhimurium population on XLD medium (♢, dotted line).

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques:

    Influence of the incubation conditions (i.e., incubation temperature and the ratio of L. monocytogenes and S . Typhimurium in the inoculum) on the cell density of the dual-species biofilm ( n = 3). Biofilms were incubated for 24 h prior to the quantification procedure. For the influence of the incubation temperature: for each ratio, significant differences have been indicated by means of capital letters, with “A” bearing the lowest value. For the influence of the inoculum ratio: for each incubation temperature, significant differences have been indicated by means of small letters, with “a” bearing the lowest value.

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Influence of the incubation conditions (i.e., incubation temperature and the ratio of L. monocytogenes and S . Typhimurium in the inoculum) on the cell density of the dual-species biofilm ( n = 3). Biofilms were incubated for 24 h prior to the quantification procedure. For the influence of the incubation temperature: for each ratio, significant differences have been indicated by means of capital letters, with “A” bearing the lowest value. For the influence of the inoculum ratio: for each incubation temperature, significant differences have been indicated by means of small letters, with “a” bearing the lowest value.

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques: Incubation

    Adherence (OD) of the dual-species biofilm as function of the incubation time ( n = 5). Biofilms were considered as strongly adherent if the OD of the sample exceeded the 4 × OD C -value (dash-dot line).

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Adherence (OD) of the dual-species biofilm as function of the incubation time ( n = 5). Biofilms were considered as strongly adherent if the OD of the sample exceeded the 4 × OD C -value (dash-dot line).

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques: Incubation

    Maturity of the dual-species biofilm as function of time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Baranyi and Roberts ( 1994 ) model are represented: total population on general medium (□, black line), L. monocytogenes population on Palcam medium (x, blue line), and S . Typhimurium population on XLD medium (◇, red line).

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Maturity of the dual-species biofilm as function of time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Baranyi and Roberts ( 1994 ) model are represented: total population on general medium (□, black line), L. monocytogenes population on Palcam medium (x, blue line), and S . Typhimurium population on XLD medium (◇, red line).

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques:

    Cell density [log 10 (CFU/cm 2 )] of the 1 and 7 day(s) old (i) dual-species biofilm (black), (ii) single-species L. monocytogenes biofilm (red), and (iii) single-species S . Typhimurium biofilm (blue) as function of the CAP treatment time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Geeraerd et al. ( 2000 ) model are represented. For the dual-species biofilm: total population on general medium (□, solid line), L. monocytogenes population on Palcam medium (x, dashed line), and S . Typhimurium population on XLD medium (♢, dotted line). For the single-species biofilms: L. monocytogenes population on Palcam medium (x, dashed line) and S . Typhimurium population on XLD medium (x, dotted line).

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Cell density [log 10 (CFU/cm 2 )] of the 1 and 7 day(s) old (i) dual-species biofilm (black), (ii) single-species L. monocytogenes biofilm (red), and (iii) single-species S . Typhimurium biofilm (blue) as function of the CAP treatment time ( n = 3). Both the experimental data (symbols) and the global fit (line) of the Geeraerd et al. ( 2000 ) model are represented. For the dual-species biofilm: total population on general medium (□, solid line), L. monocytogenes population on Palcam medium (x, dashed line), and S . Typhimurium population on XLD medium (♢, dotted line). For the single-species biofilms: L. monocytogenes population on Palcam medium (x, dashed line) and S . Typhimurium population on XLD medium (x, dotted line).

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques:

    Influence of the incubation conditions (i.e., growth medium, incubation temperature, and the ratio of L. monocytogenes and S . Typhimurium in the inoculum) on the adherence (OD) of the dual-species biofilm ( n = 3). Biofilms were incubated for 24 h prior to the quantification procedure and were considered to be strongly adherent as the average OD values were higher than their corresponding 4 × OD C -value. For the influence of the growth medium: for each temperature and each ratio, significant differences have been indicated by means of small letters, with “a” bearing the lowest value. For the influence of the incubation temperature: for each growth medium and each ratio, significant differences have been indicated by means of capital letters, with “A” bearing the lowest value. For the influence of the inoculum ratio: for each growth medium and each incubation temperature, significant differences have been indicated by means of numbers, with “1” bearing the lowest value.

    Journal: Frontiers in Microbiology

    Article Title: Dual-Species Model Biofilm Consisting of Listeria monocytogenes and Salmonella Typhimurium: Development and Inactivation With Cold Atmospheric Plasma (CAP)

    doi: 10.3389/fmicb.2019.02524

    Figure Lengend Snippet: Influence of the incubation conditions (i.e., growth medium, incubation temperature, and the ratio of L. monocytogenes and S . Typhimurium in the inoculum) on the adherence (OD) of the dual-species biofilm ( n = 3). Biofilms were incubated for 24 h prior to the quantification procedure and were considered to be strongly adherent as the average OD values were higher than their corresponding 4 × OD C -value. For the influence of the growth medium: for each temperature and each ratio, significant differences have been indicated by means of small letters, with “a” bearing the lowest value. For the influence of the incubation temperature: for each growth medium and each ratio, significant differences have been indicated by means of capital letters, with “A” bearing the lowest value. For the influence of the inoculum ratio: for each growth medium and each incubation temperature, significant differences have been indicated by means of numbers, with “1” bearing the lowest value.

    Article Snippet: Next, 2 mL of sterile PBS solution was added to the rinsed and dried biofilms and a cell scraper (blade width 20 mm, Carl Roth GmbH+Co, Germany) was used to remove the biofilm from the surface.

    Techniques: Incubation

    Biofilm produced by C. jejuni 81-176 on cover glass after 48 h at 37°C under microaerobic conditions and visualized by Field Emission Scanning Electron Microscopy. (A) C. jejuni 81-176 wild-type, (B) C. jejuni 81-176Δ cj0588 , (C) the complemented C. jejuni strain 81-176Δ cj0588 :: 0588 . Experiments were performed in triplicate and representative micrographs are shown.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Biofilm Formation and Motility Are Promoted by Cj0588-Directed Methylation of rRNA in Campylobacter jejuni

    doi: 10.3389/fcimb.2017.00533

    Figure Lengend Snippet: Biofilm produced by C. jejuni 81-176 on cover glass after 48 h at 37°C under microaerobic conditions and visualized by Field Emission Scanning Electron Microscopy. (A) C. jejuni 81-176 wild-type, (B) C. jejuni 81-176Δ cj0588 , (C) the complemented C. jejuni strain 81-176Δ cj0588 :: 0588 . Experiments were performed in triplicate and representative micrographs are shown.

    Article Snippet: Biofilms were air-dried and coated with gold-palladium (2–4 nm thick) and analyzed at nanometer image resolution by FESEM (MERLIN Carl Zeiss Germany) at 2–5 kV range accelerating voltage.

    Techniques: Produced, Electron Microscopy

    Staphylococcus aureus QS gene expression when co-cultured with P. aeruginosa on tube reactors. S. aureus biofilms were cultured in tube reactors for a period of 5 days previous to the introduction of P. aeruginosa . Once P. aeruginosa aeruginosa was introduced (day 0), samples were taken at 24 h intervals for a period of 120 h. (A) relative expression of S. aureus QS genes in dual-species biofilms compared to single species biofilms. (B) Relative expression of S. aureus single species biofilms compared to time 0. Changes of relative expression were considered significant when a twofold change was present.

    Journal: Frontiers in Microbiology

    Article Title: Maintenance of S. aureus in Co-culture With P. aeruginosa While Growing as Biofilms

    doi: 10.3389/fmicb.2018.03291

    Figure Lengend Snippet: Staphylococcus aureus QS gene expression when co-cultured with P. aeruginosa on tube reactors. S. aureus biofilms were cultured in tube reactors for a period of 5 days previous to the introduction of P. aeruginosa . Once P. aeruginosa aeruginosa was introduced (day 0), samples were taken at 24 h intervals for a period of 120 h. (A) relative expression of S. aureus QS genes in dual-species biofilms compared to single species biofilms. (B) Relative expression of S. aureus single species biofilms compared to time 0. Changes of relative expression were considered significant when a twofold change was present.

    Article Snippet: Biofilm samples were harvested with the role pin method ( ) where the biofilm paste was resuspended in 1 mL of phosphate buffer saline (PBS), homogenized for 20 sec with a tissue tearor homogenizer, serially diluted, and drop platted onto mannitol salt agar (Difco), Pseudomonas isolation agar (Difco), and 50% plate count agar (Difco).

    Techniques: Expressing, Cell Culture

    Pseudomonas aeruginosa QS gene expression when co-cultured with S. aureus on tube reactors. S. aureus biofilms were cultured in tube reactors for a period of 5 days previous to the introduction of P. aeruginosa . Once P. aeruginosa aeruginosa was introduced (day 0), samples were taken at 24 h intervals for a period of 120 h. (A) relative expression of P. aeruginosa compared to single species biofilms, (B) relative expression of P. aeruginosa QS genes in dual-species biofilms compared to day 1 of co-culture. Changes of relative expression were considered significant when a twofold change was present.

    Journal: Frontiers in Microbiology

    Article Title: Maintenance of S. aureus in Co-culture With P. aeruginosa While Growing as Biofilms

    doi: 10.3389/fmicb.2018.03291

    Figure Lengend Snippet: Pseudomonas aeruginosa QS gene expression when co-cultured with S. aureus on tube reactors. S. aureus biofilms were cultured in tube reactors for a period of 5 days previous to the introduction of P. aeruginosa . Once P. aeruginosa aeruginosa was introduced (day 0), samples were taken at 24 h intervals for a period of 120 h. (A) relative expression of P. aeruginosa compared to single species biofilms, (B) relative expression of P. aeruginosa QS genes in dual-species biofilms compared to day 1 of co-culture. Changes of relative expression were considered significant when a twofold change was present.

    Article Snippet: Biofilm samples were harvested with the role pin method ( ) where the biofilm paste was resuspended in 1 mL of phosphate buffer saline (PBS), homogenized for 20 sec with a tissue tearor homogenizer, serially diluted, and drop platted onto mannitol salt agar (Difco), Pseudomonas isolation agar (Difco), and 50% plate count agar (Difco).

    Techniques: Expressing, Cell Culture, Co-Culture Assay

    Effect of quorum sensing inactivation on the presence of S. aureus when in co-culture with P. aeruginosa . Biofilms of S. aureus were allowed to establish for a period of 5 days in microtiter plates after which, P. aeruginosa was introduced at a 1:250 ratio. P. aeruginosa strains consisted of PAO1 WT, Δ lasI , Δ lasIrhl , and Δ rhll . Upon introduction of P. aeruginosa , viability of dual-species biofilms was quantified for further 5 days. Biofilms were cultured in 10% BHI at 37°C under static conditions. Media was exchanged every 12 h. ∗ p

    Journal: Frontiers in Microbiology

    Article Title: Maintenance of S. aureus in Co-culture With P. aeruginosa While Growing as Biofilms

    doi: 10.3389/fmicb.2018.03291

    Figure Lengend Snippet: Effect of quorum sensing inactivation on the presence of S. aureus when in co-culture with P. aeruginosa . Biofilms of S. aureus were allowed to establish for a period of 5 days in microtiter plates after which, P. aeruginosa was introduced at a 1:250 ratio. P. aeruginosa strains consisted of PAO1 WT, Δ lasI , Δ lasIrhl , and Δ rhll . Upon introduction of P. aeruginosa , viability of dual-species biofilms was quantified for further 5 days. Biofilms were cultured in 10% BHI at 37°C under static conditions. Media was exchanged every 12 h. ∗ p

    Article Snippet: Biofilm samples were harvested with the role pin method ( ) where the biofilm paste was resuspended in 1 mL of phosphate buffer saline (PBS), homogenized for 20 sec with a tissue tearor homogenizer, serially diluted, and drop platted onto mannitol salt agar (Difco), Pseudomonas isolation agar (Difco), and 50% plate count agar (Difco).

    Techniques: Co-Culture Assay, Cell Culture

    Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Profiles of measured total dissolved sulfide, oxygen, pH, and calculated sulfide production rate in the biofilm. Negative depths in the profile represent the distance from the biofilm surface into the wastewater.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Model-predicted sulfate and soluble biodegradable COD profiles in the biofilm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: The SRB (A) and MA (B) proportions of total microorganisms (bacteria and archaea) detected by FISH within the sewer biofilms. C. Methanomethylophilus , “ Candidatus Methanomethylophilus.”

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay, Fluorescence In Situ Hybridization

    FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: FISH images of different sections of the sewer reactor biofilm. (A and B) Images of the biofilm sections cut perpendicularly to the substratum, with SRB in white (A) and MA in purple (B). Arrows indicate the biofilm surface. (C and D) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with SRB in white, archaea in red, and other bacteria in green, blue, and yellow. (E and F) Images of biofilm sections cut parallel to the substratum at depths of 100 μm and 700 μm, respectively, with MA in purple, other archaea in red, and bacteria in green. Scale bars, 50 μm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Fluorescence In Situ Hybridization, Sulforhodamine B Assay

    Schematic of the laboratory-scale anaerobic, annular biofilm reactor.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Schematic of the laboratory-scale anaerobic, annular biofilm reactor.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques:

    Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Comparison of model-predicted results with the experimentally measured data. (A) Relative abundances of SRB and MA. (B) Sulfide concentration profiles in the biofilm.

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay, Concentration Assay

    Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).

    Journal: Applied and Environmental Microbiology

    Article Title: Stratified Microbial Structure and Activity in Sulfide- and Methane-Producing Anaerobic Sewer Biofilms

    doi: 10.1128/AEM.02146-14

    Figure Lengend Snippet: Heat map displaying the distribution of the predominant SRB (A) and MA (B) in different biofilm layers from the biofilm surface to the bottom (Layer 1 to Layer 5).

    Article Snippet: The sectioned biofilm samples were then placed separately in 1 ml Eppendorf tubes containing 0.5 ml of phosphate-buffered saline (PBS) (containing 137 mM NaCl, 2.7 mM KCl, 10 mM Na2 HPO4 , and 2 mM KH2 PO4 ) for DNA extraction.

    Techniques: Sulforhodamine B Assay

    Confocal micrograph of a biofilm formed in a chinchilla middle ear by NTHi strain 2019 stained with MAb 6E4. The antibody was counterstained with a goat anti-mouse anti IgG antibody conjugated to fluorescein. The DNA in the biofilm was counterstained with DAPI and fluoresces blue. Organisms can be seen throughout the biofilm stained with MAb 6E4, indicating the presence of the KDO epitope in vivo .

    Journal: mBio

    Article Title: Nontypeable Haemophilus influenzae Lipooligosaccharide Expresses a Terminal Ketodeoxyoctanoate In Vivo, Which Can Be Used as a Target for Bactericidal Antibody

    doi: 10.1128/mBio.01401-18

    Figure Lengend Snippet: Confocal micrograph of a biofilm formed in a chinchilla middle ear by NTHi strain 2019 stained with MAb 6E4. The antibody was counterstained with a goat anti-mouse anti IgG antibody conjugated to fluorescein. The DNA in the biofilm was counterstained with DAPI and fluoresces blue. Organisms can be seen throughout the biofilm stained with MAb 6E4, indicating the presence of the KDO epitope in vivo .

    Article Snippet: To preserve the architecture of biofilms that had formed in vivo , we embedded the biofilm sample in an OCT compound (Fisher Scientific, Pittsburgh, PA) as previously described ( ).

    Techniques: Staining, In Vivo

    Biofilm development during microbial limitation. Confocal scanning micrographs of Clostridium thermocellum biofilms on Whatman #3 filter paper chads taken midway during the ‘biofilm invasion’ region. Low magnification images (below) show varying degrees of biofilm colonization (green) on cellulose fibers (red); where it is common to observe surface fibers with little to no biofilm growth. High magnification imaging (above) of selected heavily populated fibers shows the typical cell monolayer biofilms of this species, with cells closely lining the substratum. Dividing cells (red circles) and occasional small spore-forming cells (green dots) are observed at the surface. Cells stained with SYTO 9 (green); cellulose fibers stained with WGA-TRITC (red).

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Biofilm development during microbial limitation. Confocal scanning micrographs of Clostridium thermocellum biofilms on Whatman #3 filter paper chads taken midway during the ‘biofilm invasion’ region. Low magnification images (below) show varying degrees of biofilm colonization (green) on cellulose fibers (red); where it is common to observe surface fibers with little to no biofilm growth. High magnification imaging (above) of selected heavily populated fibers shows the typical cell monolayer biofilms of this species, with cells closely lining the substratum. Dividing cells (red circles) and occasional small spore-forming cells (green dots) are observed at the surface. Cells stained with SYTO 9 (green); cellulose fibers stained with WGA-TRITC (red).

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques: Imaging, Staining, Whole Genome Amplification

    Correlation between surface footprint area and CO 2 production. A strong positive linear correlation was observed between the measured peak rate of carbon dioxide production and the initial size of Whatman #1 sheets. This shows initial biofilm invasion proceeded to the extent at which available ‘real estate’ was provided, and that surface area was not lost before this point was reached (mainly due to the flat shape of the cellulosic chads; the sheet with the least thickness was chosen for this test). It also emphasizes the utility of such measurements for comparing the degree of bacterium-accessible surface area of complex and heterogeneous substrates. Slope p = 0.000, constant p = 0.560.

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Correlation between surface footprint area and CO 2 production. A strong positive linear correlation was observed between the measured peak rate of carbon dioxide production and the initial size of Whatman #1 sheets. This shows initial biofilm invasion proceeded to the extent at which available ‘real estate’ was provided, and that surface area was not lost before this point was reached (mainly due to the flat shape of the cellulosic chads; the sheet with the least thickness was chosen for this test). It also emphasizes the utility of such measurements for comparing the degree of bacterium-accessible surface area of complex and heterogeneous substrates. Slope p = 0.000, constant p = 0.560.

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques:

    Conversion efficiency during microbial limitation. (A) . Measurement of CO 2 production as an indication of biofilm development rate, and the peak activity on three cellulosic substrates with equal size, but different mass. (B) . Comparison of average conversion efficiency during the initial microbial limitation zone. A doubling in rates of gas production is understood as a doubling of sessile population size, and peak rates are strongly influenced by availability of attachment surface area. The combination of these factors reveals the average conversion efficiency during microbial limitation and it becomes an indicator of biofilm colonization potential (higher is better). Error bars show standard deviation.

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Conversion efficiency during microbial limitation. (A) . Measurement of CO 2 production as an indication of biofilm development rate, and the peak activity on three cellulosic substrates with equal size, but different mass. (B) . Comparison of average conversion efficiency during the initial microbial limitation zone. A doubling in rates of gas production is understood as a doubling of sessile population size, and peak rates are strongly influenced by availability of attachment surface area. The combination of these factors reveals the average conversion efficiency during microbial limitation and it becomes an indicator of biofilm colonization potential (higher is better). Error bars show standard deviation.

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques: Activity Assay, Standard Deviation

    Biofilm to planktonic cell yield. Numbers of cells in reactor effluent as indication of biofilm-to-planktonic cell yield and corresponding (matching) CO 2 production rate during the microbial limitation period and a few hours into plateau.

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Biofilm to planktonic cell yield. Numbers of cells in reactor effluent as indication of biofilm-to-planktonic cell yield and corresponding (matching) CO 2 production rate during the microbial limitation period and a few hours into plateau.

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques:

    Model CO 2 profile. Typical measurement of changes in carbon dioxide production rates during microbial conversion of a Whatman #3 paper chad cut at 6600 mm 2 footprint area (value accounts for both sides of the paper). The working definitions established and used throughout this paper are labeled and delineated: the lag phase from the moment of inoculation varies between seven to nine hours; start of growth is considered at 5 × 10 -5 mmoles/min carbon dioxide rate and the fermentation end-point at 10 × 10 -5 mmoles/min; the initial growth period is termed the ‘biofilm invasion’ region, which ends when near-all of accessible surface area (i.e., the ‘real estate’) of the paper has been colonized; it is followed by a ‘plateau region’ of stable, and maximal carbon dioxide output where biofilms advance through the depth of the paper chads (new surfaces become available at the same rate that colonized surfaces are depleted); the last ‘degradation’ region is characterized by rapid loss of available surface and chad integrity.

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Model CO 2 profile. Typical measurement of changes in carbon dioxide production rates during microbial conversion of a Whatman #3 paper chad cut at 6600 mm 2 footprint area (value accounts for both sides of the paper). The working definitions established and used throughout this paper are labeled and delineated: the lag phase from the moment of inoculation varies between seven to nine hours; start of growth is considered at 5 × 10 -5 mmoles/min carbon dioxide rate and the fermentation end-point at 10 × 10 -5 mmoles/min; the initial growth period is termed the ‘biofilm invasion’ region, which ends when near-all of accessible surface area (i.e., the ‘real estate’) of the paper has been colonized; it is followed by a ‘plateau region’ of stable, and maximal carbon dioxide output where biofilms advance through the depth of the paper chads (new surfaces become available at the same rate that colonized surfaces are depleted); the last ‘degradation’ region is characterized by rapid loss of available surface and chad integrity.

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques: Labeling

    Biofilm development during substrate limitation. Confocal scanning micrographs of C. thermocellum biofilms on Whatman #3 filter paper chads, taken approximately halfway through the ‘plateau’ (see figure 3 ) region. Low magnification images (below) show heavily populated fibers, some with very high cell-density biofilms, which were consistently observed throughout. Fibers with lesser colonization were observed typically deeper into the paper structure. High magnification imaging (above) of an extremely dense region shows the formation of numerous terminal sporangia, attached to the substratum at the non-sporulated end. Normal cells are still observed to line the surface of the same fibers. The regions indicated with white arrows show near-complete collapse of the cellulose fibers. Cells stained with SYTO 9 (green); cellulose fibers stained with WGA-TRITC (red).

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Biofilm development during substrate limitation. Confocal scanning micrographs of C. thermocellum biofilms on Whatman #3 filter paper chads, taken approximately halfway through the ‘plateau’ (see figure 3 ) region. Low magnification images (below) show heavily populated fibers, some with very high cell-density biofilms, which were consistently observed throughout. Fibers with lesser colonization were observed typically deeper into the paper structure. High magnification imaging (above) of an extremely dense region shows the formation of numerous terminal sporangia, attached to the substratum at the non-sporulated end. Normal cells are still observed to line the surface of the same fibers. The regions indicated with white arrows show near-complete collapse of the cellulose fibers. Cells stained with SYTO 9 (green); cellulose fibers stained with WGA-TRITC (red).

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques: Imaging, Staining, Whole Genome Amplification

    Substrate heterogeneity. Micrographs of Whatman filter paper showing highly heterogeneous fiber distribution, pores and channels, which make quantitative differentiation of inner structure properties and of cellulose area available for microbial adhesion not possible. Images taken with confocal reflection microscopy of paper chads sputter-coated with gold. In the current study we refer to biofilm ‘real-estate’ as the portion of the cellulose surface that is accessible to microbial adhesion.

    Journal: Biotechnology for Biofuels

    Article Title: Tracking the cellulolytic activity of Clostridium thermocellum biofilms

    doi: 10.1186/1754-6834-6-175

    Figure Lengend Snippet: Substrate heterogeneity. Micrographs of Whatman filter paper showing highly heterogeneous fiber distribution, pores and channels, which make quantitative differentiation of inner structure properties and of cellulose area available for microbial adhesion not possible. Images taken with confocal reflection microscopy of paper chads sputter-coated with gold. In the current study we refer to biofilm ‘real-estate’ as the portion of the cellulose surface that is accessible to microbial adhesion.

    Article Snippet: The rate of cell elution from biofilms growing on Whatman #3 chads was measured in parallel with on-line rates of CO2 production (Figure ).

    Techniques: Microscopy

    Cinnamomum zeylanicum Blume EO inhibitory effect on biofilm formation and mature biofilm reduction (G1: 24-h contact with EO; G2: 48-h contact with EO) corresponding to (a) Candida albicans ATCC 60193; (b) Candida tropicalis ATCC 750; and (c) Candida spp. multispecies ( Candida albicans ATCC 60193 and Candida tropicalis ATCC 750). ∗ Significant biofilm reduction (Kruskal-Wallis test followed by Dunn's post hoc test, p

    Journal: Evidence-based Complementary and Alternative Medicine : eCAM

    Article Title: In Vitro Effect of Cinnamomum zeylanicum Blume Essential Oil on Candida spp. Involved in Oral Infections

    doi: 10.1155/2018/4045013

    Figure Lengend Snippet: Cinnamomum zeylanicum Blume EO inhibitory effect on biofilm formation and mature biofilm reduction (G1: 24-h contact with EO; G2: 48-h contact with EO) corresponding to (a) Candida albicans ATCC 60193; (b) Candida tropicalis ATCC 750; and (c) Candida spp. multispecies ( Candida albicans ATCC 60193 and Candida tropicalis ATCC 750). ∗ Significant biofilm reduction (Kruskal-Wallis test followed by Dunn's post hoc test, p

    Article Snippet: Significant differences between the controls and test substance in the kinetic, biofilm, and PBMC cytotoxicity assays were assessed with the Kruskal-Wallis test followed by Dunn's post hoc test ( α = 0.05) using GraphPad Prism version 7.0 (San Diego, CA, USA).

    Techniques:

    Nystatin inhibitory effect on biofilm formation and mature biofilm reduction (G1: 24-h contact with EO and G2: 48-h contact with EO) corresponding to (a) Candida albicans ATCC 60193; (b) Candida tropicalis ATCC 750; and (c) Candida spp. multispecies ( Candida albicans ATCC 60193 and Candida tropicalis ATCC 750). ∗ Significant biofilm reduction (Kruskal-Wallis test followed by Dunn's post hoc test, p

    Journal: Evidence-based Complementary and Alternative Medicine : eCAM

    Article Title: In Vitro Effect of Cinnamomum zeylanicum Blume Essential Oil on Candida spp. Involved in Oral Infections

    doi: 10.1155/2018/4045013

    Figure Lengend Snippet: Nystatin inhibitory effect on biofilm formation and mature biofilm reduction (G1: 24-h contact with EO and G2: 48-h contact with EO) corresponding to (a) Candida albicans ATCC 60193; (b) Candida tropicalis ATCC 750; and (c) Candida spp. multispecies ( Candida albicans ATCC 60193 and Candida tropicalis ATCC 750). ∗ Significant biofilm reduction (Kruskal-Wallis test followed by Dunn's post hoc test, p

    Article Snippet: Significant differences between the controls and test substance in the kinetic, biofilm, and PBMC cytotoxicity assays were assessed with the Kruskal-Wallis test followed by Dunn's post hoc test ( α = 0.05) using GraphPad Prism version 7.0 (San Diego, CA, USA).

    Techniques:

    The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species biofilms of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).

    Journal: PLoS ONE

    Article Title: Nanoparticle-Encapsulated Chlorhexidine against Oral Bacterial Biofilms

    doi: 10.1371/journal.pone.0103234

    Figure Lengend Snippet: The antibacterial effects of Nano-CHX treatment for 24 h on the mixed-species biofilms of S. sobrinus , F. nucleatum and P. gingivalis . Representative scanning electron microscopy images: B vs. A (blank nanoparticles); and confocal laser scanning microscopy images: D vs. C (blank nanoparticles).

    Article Snippet: The topographic features of each biofilm were visualized with a SEM (Hitachi S-3400N SEM at EM Unit, HKU) in high vacuum mode at 10 kV.

    Techniques: Electron Microscopy, Confocal Laser Scanning Microscopy

    Quantitative analysis of macrophage migration within 48 h biofilms prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Quantitative analysis of macrophage migration within 48 h biofilms prepared from C. albicans strains CAI4, pmr1 Δ, and pmr1 Δ+ PMR1 . The chart shows mean relative macrophage velocity + SD relative to macrophage velocity of J774.1 macrophages added in suspension to CAI4 (wild type biofilms). Migration data over a 30 min period are shown. No statistical significance of mean differences was determined using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests.

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Migration

    Representative single time point images acquired using Volocity software, showing J774.1 macrophages stained with LysoTracker Red (LTR; red), and C. albicans stained with Calcofluor White (CFW; blue). Macrophages were added in suspension to ( a ) planktonic yeast (40× objective), or ( b ) and ( c ) 48 h biofilms (20× objective); presented with ( a ) and ( b ) opacity 3D rendering, and ( c ) x , y and z at 20 μm depth. White grid unit or bar represents ( a ) 18.05 μm, ( b ) 36.17 μm, and ( c ) 40 μm.

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Representative single time point images acquired using Volocity software, showing J774.1 macrophages stained with LysoTracker Red (LTR; red), and C. albicans stained with Calcofluor White (CFW; blue). Macrophages were added in suspension to ( a ) planktonic yeast (40× objective), or ( b ) and ( c ) 48 h biofilms (20× objective); presented with ( a ) and ( b ) opacity 3D rendering, and ( c ) x , y and z at 20 μm depth. White grid unit or bar represents ( a ) 18.05 μm, ( b ) 36.17 μm, and ( c ) 40 μm.

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Software, Staining

    Quantitative analysis of macrophage migration in the presence of different wildtype C. albicans . This chart shows mean relative macrophage velocity + SD, relative to macrophage velocity of pre-adhered J774.1 (Adh-macs) responding to planktonic yeast. Relative velocities of J774.1 macrophages added in suspension (Susp-macs) to either yeast or a 48 h biofilm over a 30 min period are shown. Statistical significance was evaluated using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests. ** p

    Journal: Journal of Fungi

    Article Title: Macrophage Migration Is Impaired within Candida albicans Biofilms

    doi: 10.3390/jof3030031

    Figure Lengend Snippet: Quantitative analysis of macrophage migration in the presence of different wildtype C. albicans . This chart shows mean relative macrophage velocity + SD, relative to macrophage velocity of pre-adhered J774.1 (Adh-macs) responding to planktonic yeast. Relative velocities of J774.1 macrophages added in suspension (Susp-macs) to either yeast or a 48 h biofilm over a 30 min period are shown. Statistical significance was evaluated using one-way analysis of variance (ANOVA) and Tukey Multiple Analysis Comparison Tests. ** p

    Article Snippet: Biofilms were prepared by seeding µ-Slide 8-well chambers (ibidi GmbH, Munich, Germany) with 3 × 105 Leicestershire live C. albicans yeast in Dulbecco’s Modified Eagle Medium (DMEM; Lonza, Slough, UK), supplemented with 10% (v /v ) heat-inactivated FCS (Biosera, Ringmer, UK), 200 U/mL penicillin/streptomycin antibiotics (Invitrogen, Paisley, UK), and 2 mM L-glutamine (Invitrogen, Paisley, UK), at 37 °C for 48 h. There were two assay designs, with planktonic yeast added to either imaging dishes containing macrophages, or to fungal biofilms with macrophages added in.

    Techniques: Migration, Magnetic Cell Separation

    Functional annotation of differentially expressed genes reveals upregulation of drug transporters. Gene distribution of significantly upregulated C. auris genes in 24-h biofilms relative to planktonic cells, grouped into biological process (BP), cellular component (CC), and metabolic function (MF) gene ontology categories (A). Log 2 fold change of upregulated ABC and MFS drug transporters within 24-h biofilms (B). All GO terms have a P value of

    Journal: mSphere

    Article Title: Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance

    doi: 10.1128/mSphere.00334-18

    Figure Lengend Snippet: Functional annotation of differentially expressed genes reveals upregulation of drug transporters. Gene distribution of significantly upregulated C. auris genes in 24-h biofilms relative to planktonic cells, grouped into biological process (BP), cellular component (CC), and metabolic function (MF) gene ontology categories (A). Log 2 fold change of upregulated ABC and MFS drug transporters within 24-h biofilms (B). All GO terms have a P value of

    Article Snippet: Biofilms were grown as described above in 75-cm3 ) before sequencing using the HiSeq 2500 Illumina sequencer.

    Techniques: Functional Assay

    Formation and development of Candida auris biofilms. Schematic representation of the transcriptional mediators of the three main stages of C. auris biofilm development: adherence of yeast cells to surface (early phase), proliferation (intermediate phase), and maturation into a structured biofilm (mature phase).

    Journal: mSphere

    Article Title: Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance

    doi: 10.1128/mSphere.00334-18

    Figure Lengend Snippet: Formation and development of Candida auris biofilms. Schematic representation of the transcriptional mediators of the three main stages of C. auris biofilm development: adherence of yeast cells to surface (early phase), proliferation (intermediate phase), and maturation into a structured biofilm (mature phase).

    Article Snippet: Biofilms were grown as described above in 75-cm3 ) before sequencing using the HiSeq 2500 Illumina sequencer.

    Techniques:

    Candida auris biofilm development correlates with increased antifungal tolerance. Candida auris biofilms were standardized at 1 × 10 6 CFU/ml and grown for 4, 12, and 24 h. Biofilm biomass was then quantified using the crystal violet assay, with the composition of biofilm cells enumerated using qPCR and represented by a box-and-whisker plot as the total biomass of four C. auris isolates (A, left y axis). Planktonic susceptibility testing was performed against serially diluted miconazole, micafungin, and amphotericin B concentrations using the CLSI guidelines, with biofilm susceptibility testing performed using the XTT assay and with median MIC values plotted (A, right y axis). In addition, biofilms were grown, fixed, and processed for SEM before imaging using a JEOL-JSM-6400 scanning electron microscope. Micrographs represent lower magnification (×1,000) and higher magnification (inset, ×5,000) of biofilms grown for 4 h (Bi), 12 h (Bii), and 24 h (Biii).

    Journal: mSphere

    Article Title: Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance

    doi: 10.1128/mSphere.00334-18

    Figure Lengend Snippet: Candida auris biofilm development correlates with increased antifungal tolerance. Candida auris biofilms were standardized at 1 × 10 6 CFU/ml and grown for 4, 12, and 24 h. Biofilm biomass was then quantified using the crystal violet assay, with the composition of biofilm cells enumerated using qPCR and represented by a box-and-whisker plot as the total biomass of four C. auris isolates (A, left y axis). Planktonic susceptibility testing was performed against serially diluted miconazole, micafungin, and amphotericin B concentrations using the CLSI guidelines, with biofilm susceptibility testing performed using the XTT assay and with median MIC values plotted (A, right y axis). In addition, biofilms were grown, fixed, and processed for SEM before imaging using a JEOL-JSM-6400 scanning electron microscope. Micrographs represent lower magnification (×1,000) and higher magnification (inset, ×5,000) of biofilms grown for 4 h (Bi), 12 h (Bii), and 24 h (Biii).

    Article Snippet: Biofilms were grown as described above in 75-cm3 ) before sequencing using the HiSeq 2500 Illumina sequencer.

    Techniques: Crystal Violet Assay, Real-time Polymerase Chain Reaction, Whisker Assay, XTT Assay, Imaging, Microscopy