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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 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation"

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

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00853

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.
Figure Legend 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.

Techniques Used:

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.
Figure Legend 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.

Techniques Used: 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.
Figure Legend 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.

Techniques Used: Fluorescence, Stripping Membranes

2) Product Images from "Mechanisms of post-transcriptional gene regulation in bacterial biofilms"

Article Title: Mechanisms of post-transcriptional gene regulation in bacterial biofilms

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2014.00038

Post-transcriptional regulatory networks directing biofilm formation . Numerous post-transcriptional regulatory factors, mainly affecting biofilm maturation at the level of synthesis or exopolysaccharides has been described currently and are represented here. The RNA-binding protein , CsrA, represses biofilm formation by directly and indirectly affecting stability of mRNA transcripts encoding important polysaccharides constituting the extracellular biofilm matrix. CsrA acts alternately by repressing GGDEF/EAL encoding proteins which determine c-di-GMP levels , or by favoring motility, rather than biofilm formation, by stabilizing transcripts encoding the master regulator of flagella, FlhDC. Several ncRNAs (OmrA/B, RprA, GcvB, McaS) regulate biofilm by repressing csgD , encoding the CsgD master regulator involved in the production of curli fimbria, cellulose, and c-di-GMP. Other ncRNAs (CsrB/CsrC, McaS) favor biofilm formation by blocking CsrA activity (e.g., in E. coli and Salmonella ) or by positively affecting production of c-di-GMP (Qrr1-4) and expression of exopolysaccharides (e.g., V. cholerae ). To exert their function, many of these sRNAs need to be bound to the RNA-binding chaperone Hfq, which has been reported to also repress biofilm by affecting the expression of the GGDEF protein, HmsT ( Y. pestis ), required to synthesize c-di-GMP. Changes in the levels of c-di-GMP are sensed by the GEMM riboswitch which leads to regulation of organelle biosynthesis that promotes the transformation between motile and sessile lifestyles, where increased c-di-GMP leads to increased biofilm formation and vice versa . The RNases E and G mainly cause the decay of ncRNAs that are involved in the biofilm formation. Degradation of the antitoxin mqsA transcript by the MqsR toxin, leads to inhibition of motility, and induction of csgD , favoring both curli and cellulose production. Environmental factors such as nutrient concentrations (glucose, amino acids) and other physiological stresses (osmolarity, pH, oxidative stress, antimicrobials) are important signals mediating the switch from the planktonic motile to sessile biofilm lifestyles. RNA-binding proteins are shown in orange, ncRNAs are shown in green, riboswitches are shown in pink, TA systems are shown in dark blue and RNases are shown in violet. CsgD, FlhDC, NhaR, and RpoS are major transcriptional regulators. Cellulose, PGA and EPS are expolysaccharides. Hard arrows indicate a direct or indirect positive effect, while truncated arrows indicate a direct or indirect negative effect. Black arrows show those mechanisms that are present in E. coli and are shared in many other pathogens, while red arrows show those mechanism that are present in specific microorganisms (see text for details).
Figure Legend Snippet: Post-transcriptional regulatory networks directing biofilm formation . Numerous post-transcriptional regulatory factors, mainly affecting biofilm maturation at the level of synthesis or exopolysaccharides has been described currently and are represented here. The RNA-binding protein , CsrA, represses biofilm formation by directly and indirectly affecting stability of mRNA transcripts encoding important polysaccharides constituting the extracellular biofilm matrix. CsrA acts alternately by repressing GGDEF/EAL encoding proteins which determine c-di-GMP levels , or by favoring motility, rather than biofilm formation, by stabilizing transcripts encoding the master regulator of flagella, FlhDC. Several ncRNAs (OmrA/B, RprA, GcvB, McaS) regulate biofilm by repressing csgD , encoding the CsgD master regulator involved in the production of curli fimbria, cellulose, and c-di-GMP. Other ncRNAs (CsrB/CsrC, McaS) favor biofilm formation by blocking CsrA activity (e.g., in E. coli and Salmonella ) or by positively affecting production of c-di-GMP (Qrr1-4) and expression of exopolysaccharides (e.g., V. cholerae ). To exert their function, many of these sRNAs need to be bound to the RNA-binding chaperone Hfq, which has been reported to also repress biofilm by affecting the expression of the GGDEF protein, HmsT ( Y. pestis ), required to synthesize c-di-GMP. Changes in the levels of c-di-GMP are sensed by the GEMM riboswitch which leads to regulation of organelle biosynthesis that promotes the transformation between motile and sessile lifestyles, where increased c-di-GMP leads to increased biofilm formation and vice versa . The RNases E and G mainly cause the decay of ncRNAs that are involved in the biofilm formation. Degradation of the antitoxin mqsA transcript by the MqsR toxin, leads to inhibition of motility, and induction of csgD , favoring both curli and cellulose production. Environmental factors such as nutrient concentrations (glucose, amino acids) and other physiological stresses (osmolarity, pH, oxidative stress, antimicrobials) are important signals mediating the switch from the planktonic motile to sessile biofilm lifestyles. RNA-binding proteins are shown in orange, ncRNAs are shown in green, riboswitches are shown in pink, TA systems are shown in dark blue and RNases are shown in violet. CsgD, FlhDC, NhaR, and RpoS are major transcriptional regulators. Cellulose, PGA and EPS are expolysaccharides. Hard arrows indicate a direct or indirect positive effect, while truncated arrows indicate a direct or indirect negative effect. Black arrows show those mechanisms that are present in E. coli and are shared in many other pathogens, while red arrows show those mechanism that are present in specific microorganisms (see text for details).

Techniques Used: RNA Binding Assay, Blocking Assay, Activity Assay, Expressing, Transformation Assay, Inhibition

3) Product Images from "Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation"

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

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2018.00853

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.
Figure Legend 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.

Techniques Used: Fluorescence, Stripping Membranes

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.
Figure Legend 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.

Techniques Used:

4) Product Images from "The Second Skin: Ecological Role of Epibiotic Biofilms on Marine Organisms"

Article Title: The Second Skin: Ecological Role of Epibiotic Biofilms on Marine Organisms

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2012.00292

Summary of biofilm impact on the host varying from detrimental to beneficial effects according to the epibiont’s identity, the type of interaction considered and the environmental conditions . Via a recruitment/detachment equilibrium – controlled by environmental and host traits – epibiotic bacterial communities are connected to the free water phase. When forming a biofilm, bacteria experience a boost in activity and interactions. The host will experience a certain reduction in irradiation. Fouling, infections and predation will be affected by the presence of a biofilm, but extent and even sign of these effects are context-specific. An algal host will experience a reduction or an enhancement in nutrient availability depending on whether the autotrophic, respectively heterotrophic components prevail in the biofilm. Wastes and secondary metabolites (including infochemicals) may be metabilized by the biofilm.
Figure Legend Snippet: Summary of biofilm impact on the host varying from detrimental to beneficial effects according to the epibiont’s identity, the type of interaction considered and the environmental conditions . Via a recruitment/detachment equilibrium – controlled by environmental and host traits – epibiotic bacterial communities are connected to the free water phase. When forming a biofilm, bacteria experience a boost in activity and interactions. The host will experience a certain reduction in irradiation. Fouling, infections and predation will be affected by the presence of a biofilm, but extent and even sign of these effects are context-specific. An algal host will experience a reduction or an enhancement in nutrient availability depending on whether the autotrophic, respectively heterotrophic components prevail in the biofilm. Wastes and secondary metabolites (including infochemicals) may be metabilized by the biofilm.

Techniques Used: Activity Assay, Irradiation

5) Product Images from "Genetic control of bacterial biofilms"

Article Title: Genetic control of bacterial biofilms

Journal: Journal of Applied Genetics

doi: 10.1007/s13353-015-0309-2

Control of biofilm formation in S. aureus and S. Typhimurium. S. aureus : biofilm control by five main regulatory factors is shown. QS positively regulates the synthesis of detergent-like peptides, proteases, and nucleases, resulting in biofilm dispersal. The involvement of c-di-GMP and sRNAs in biofilm regulation is still controversial, and the mechanism of their activity is unknown. SarA inhibits the expression of proteases and nucleases and, thus, promotes the development of immature biofilm. Alternative sigma factor SigB promotes the expression of adherence factors and, thus, positively regulates the initial steps of biofilm formation. S. Typhimurium: c-di-GMP activates the master CsgD and, subsequently, increases the synthesis of curli, Bap, and cellulose. Several sRNAs (McaS, RprA, OmrA/B, and possibly GcvB) inhibit the translation of CsgD mRNA and inhibit biofilm development
Figure Legend Snippet: Control of biofilm formation in S. aureus and S. Typhimurium. S. aureus : biofilm control by five main regulatory factors is shown. QS positively regulates the synthesis of detergent-like peptides, proteases, and nucleases, resulting in biofilm dispersal. The involvement of c-di-GMP and sRNAs in biofilm regulation is still controversial, and the mechanism of their activity is unknown. SarA inhibits the expression of proteases and nucleases and, thus, promotes the development of immature biofilm. Alternative sigma factor SigB promotes the expression of adherence factors and, thus, positively regulates the initial steps of biofilm formation. S. Typhimurium: c-di-GMP activates the master CsgD and, subsequently, increases the synthesis of curli, Bap, and cellulose. Several sRNAs (McaS, RprA, OmrA/B, and possibly GcvB) inhibit the translation of CsgD mRNA and inhibit biofilm development

Techniques Used: Activity Assay, Expressing

Control of biofilm formation in P. aeruginosa . Three control pathways are shown. In two AHL-based QS pathways, cell density plays a role of the environmental signal. The signal is then transferred through the transmitter proteins LasI and RhlI to the effector proteins LasR and RhlR, being transcriptional regulators. The QS system controls the synthesis of rhamnolipids and secretion of eDNA. In c-di-GMP signaling, the level of c-di-GMP is sensed by sensor proteins—receptors which govern the metabolism of this molecule through the activity of diguanylate cyclases (DCGs) and phosphodiesterases (PDEs). Upon binding to the effector proteins, which are activators or repressors acting at transcriptional or post-transcriptional levels, c-di-GMP controls the synthesis of adhesins and exopolysaccharides and inhibits the motility. The control by sRNA involves the activation of sensor kinases, e.g., GacS, which phosphorylates transmitter protein GacA, leading to the subsequent activation of small RNAs, inhibition of effector RsmA activity, and, finally, to the inhibition of exopolysaccharides synthesis and enhancement of motility
Figure Legend Snippet: Control of biofilm formation in P. aeruginosa . Three control pathways are shown. In two AHL-based QS pathways, cell density plays a role of the environmental signal. The signal is then transferred through the transmitter proteins LasI and RhlI to the effector proteins LasR and RhlR, being transcriptional regulators. The QS system controls the synthesis of rhamnolipids and secretion of eDNA. In c-di-GMP signaling, the level of c-di-GMP is sensed by sensor proteins—receptors which govern the metabolism of this molecule through the activity of diguanylate cyclases (DCGs) and phosphodiesterases (PDEs). Upon binding to the effector proteins, which are activators or repressors acting at transcriptional or post-transcriptional levels, c-di-GMP controls the synthesis of adhesins and exopolysaccharides and inhibits the motility. The control by sRNA involves the activation of sensor kinases, e.g., GacS, which phosphorylates transmitter protein GacA, leading to the subsequent activation of small RNAs, inhibition of effector RsmA activity, and, finally, to the inhibition of exopolysaccharides synthesis and enhancement of motility

Techniques Used: Activity Assay, Binding Assay, Activation Assay, Inhibition

Subsequent stages of bacterial biofilm formation/dispersal and their genetic regulation. (i) reversible, followed by irreversible, attachment to the surface, (ii) formation of microcolonies, (iii and iv) biofilm maturation leading to the formation of bacterial consortia, and (v) biofilm dispersal. The regulatory involvement of quorum sensing (QS), bis-(3’-5’)-cyclic diguanosine monophosphate (c-di-GMP), and small RNAs (sRNAs) is shown by the arrows
Figure Legend Snippet: Subsequent stages of bacterial biofilm formation/dispersal and their genetic regulation. (i) reversible, followed by irreversible, attachment to the surface, (ii) formation of microcolonies, (iii and iv) biofilm maturation leading to the formation of bacterial consortia, and (v) biofilm dispersal. The regulatory involvement of quorum sensing (QS), bis-(3’-5’)-cyclic diguanosine monophosphate (c-di-GMP), and small RNAs (sRNAs) is shown by the arrows

Techniques Used:

Control of biofilm development in Vibrio cholerae at low cell density. At low concentration of autoinducers, histidine kinases LuxP and CpqS are phosphorylated and able to phosphorylate regulator LuxO. LuxO–P activate the expression of Qrr 1–4 RNAs, which, in turn, positively influence the level of c-di-GMP. c-di-GMP activates VpsR and VpsT proteins, which positively regulate biofilm genes
Figure Legend Snippet: Control of biofilm development in Vibrio cholerae at low cell density. At low concentration of autoinducers, histidine kinases LuxP and CpqS are phosphorylated and able to phosphorylate regulator LuxO. LuxO–P activate the expression of Qrr 1–4 RNAs, which, in turn, positively influence the level of c-di-GMP. c-di-GMP activates VpsR and VpsT proteins, which positively regulate biofilm genes

Techniques Used: Concentration Assay, Expressing

6) Product Images from "Systemic Responses of Barley to the 3-hydroxy-decanoyl-homoserine Lactone Producing Plant Beneficial Endophyte Acidovorax radicis N35"

Article Title: Systemic Responses of Barley to the 3-hydroxy-decanoyl-homoserine Lactone Producing Plant Beneficial Endophyte Acidovorax radicis N35

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2016.01868

Colonization of barley roots by fluorescence labeled A . radicis N35 wild type and araI mutant detected using CLSM lambda mode . Blue color represent barley roots, red color represent the YFP-labeled A. radicis N35 wild type and green color represents the GFP labeled A. radicis N35 araI::tet AHL mutant. (A) YFP-labeled A. radicis N35 forms biofilm in the main root part and root hair part. (B) GFP-labeled A. radicis N35 araI::tet . (C,D) Inoculation with GFP-labeled A. radicis N35 araI::tet mutant mixed 1:1 with YFP-labeled A. radicis N35 wild type.
Figure Legend Snippet: Colonization of barley roots by fluorescence labeled A . radicis N35 wild type and araI mutant detected using CLSM lambda mode . Blue color represent barley roots, red color represent the YFP-labeled A. radicis N35 wild type and green color represents the GFP labeled A. radicis N35 araI::tet AHL mutant. (A) YFP-labeled A. radicis N35 forms biofilm in the main root part and root hair part. (B) GFP-labeled A. radicis N35 araI::tet . (C,D) Inoculation with GFP-labeled A. radicis N35 araI::tet mutant mixed 1:1 with YFP-labeled A. radicis N35 wild type.

Techniques Used: Fluorescence, Labeling, Mutagenesis, Confocal Laser Scanning Microscopy

7) Product Images from "A Bacillus subtilis Sensor Kinase Involved in Triggering Biofilm Formation on the Roots of Tomato Plants"

Article Title: A Bacillus subtilis Sensor Kinase Involved in Triggering Biofilm Formation on the Roots of Tomato Plants

Journal: Molecular microbiology

doi: 10.1111/j.1365-2958.2012.08109.x

Biofilm formation by various kinase mutants on tomato roots
Figure Legend Snippet: Biofilm formation by various kinase mutants on tomato roots

Techniques Used:

l -Malic acid stimulates biofilm formation
Figure Legend Snippet: l -Malic acid stimulates biofilm formation

Techniques Used:

B. subtilis forms biofilms on the tomato root surfaces
Figure Legend Snippet: B. subtilis forms biofilms on the tomato root surfaces

Techniques Used:

Related Articles

Plasmid Preparation:

Article Title: Systemic Responses of Barley to the 3-hydroxy-decanoyl-homoserine Lactone Producing Plant Beneficial Endophyte Acidovorax radicis N35
Article Snippet: .. AHLs dependent QS circuits are global regulons; they control a wide range of biological functions including swarming motility, bioluminescence, plasmid conjugative transfer, biofilm formation, antibiotic biosynthesis, and the production of virulence factors in plant and animal pathogens (Eberl, ; Waters and Bassler, ). .. Since these AHL autoinducers also convey information about the surrounding and habitat quality of the cells, AHLs play a central role in optimizing the expression of their genetic repertoire and thus have an important efficiency optimizing function (Hense et al., ).

Expressing:

Article Title: Mechanisms of post-transcriptional gene regulation in bacterial biofilms
Article Snippet: .. Employing ncRNAs to fine-tune the expression of genes, stabilize mRNA, and regulate biofilm formation is an energetically economical strategy (Waters and Storz, ). .. Synthesis of ncRNA is part of the on-going transcription process and likely does not require any additional enzymatic processing as far as is known, therefore defeating the requirement for additional proteins to be synthesized.

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    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 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biofilm formation/product/Waters Corporation
    Average 92 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    biofilm formation - by Bioz Stars, 2020-05
    92/100 stars
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    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

    Post-transcriptional regulatory networks directing biofilm formation . Numerous post-transcriptional regulatory factors, mainly affecting biofilm maturation at the level of synthesis or exopolysaccharides has been described currently and are represented here. The RNA-binding protein , CsrA, represses biofilm formation by directly and indirectly affecting stability of mRNA transcripts encoding important polysaccharides constituting the extracellular biofilm matrix. CsrA acts alternately by repressing GGDEF/EAL encoding proteins which determine c-di-GMP levels , or by favoring motility, rather than biofilm formation, by stabilizing transcripts encoding the master regulator of flagella, FlhDC. Several ncRNAs (OmrA/B, RprA, GcvB, McaS) regulate biofilm by repressing csgD , encoding the CsgD master regulator involved in the production of curli fimbria, cellulose, and c-di-GMP. Other ncRNAs (CsrB/CsrC, McaS) favor biofilm formation by blocking CsrA activity (e.g., in E. coli and Salmonella ) or by positively affecting production of c-di-GMP (Qrr1-4) and expression of exopolysaccharides (e.g., V. cholerae ). To exert their function, many of these sRNAs need to be bound to the RNA-binding chaperone Hfq, which has been reported to also repress biofilm by affecting the expression of the GGDEF protein, HmsT ( Y. pestis ), required to synthesize c-di-GMP. Changes in the levels of c-di-GMP are sensed by the GEMM riboswitch which leads to regulation of organelle biosynthesis that promotes the transformation between motile and sessile lifestyles, where increased c-di-GMP leads to increased biofilm formation and vice versa . The RNases E and G mainly cause the decay of ncRNAs that are involved in the biofilm formation. Degradation of the antitoxin mqsA transcript by the MqsR toxin, leads to inhibition of motility, and induction of csgD , favoring both curli and cellulose production. Environmental factors such as nutrient concentrations (glucose, amino acids) and other physiological stresses (osmolarity, pH, oxidative stress, antimicrobials) are important signals mediating the switch from the planktonic motile to sessile biofilm lifestyles. RNA-binding proteins are shown in orange, ncRNAs are shown in green, riboswitches are shown in pink, TA systems are shown in dark blue and RNases are shown in violet. CsgD, FlhDC, NhaR, and RpoS are major transcriptional regulators. Cellulose, PGA and EPS are expolysaccharides. Hard arrows indicate a direct or indirect positive effect, while truncated arrows indicate a direct or indirect negative effect. Black arrows show those mechanisms that are present in E. coli and are shared in many other pathogens, while red arrows show those mechanism that are present in specific microorganisms (see text for details).

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Mechanisms of post-transcriptional gene regulation in bacterial biofilms

    doi: 10.3389/fcimb.2014.00038

    Figure Lengend Snippet: Post-transcriptional regulatory networks directing biofilm formation . Numerous post-transcriptional regulatory factors, mainly affecting biofilm maturation at the level of synthesis or exopolysaccharides has been described currently and are represented here. The RNA-binding protein , CsrA, represses biofilm formation by directly and indirectly affecting stability of mRNA transcripts encoding important polysaccharides constituting the extracellular biofilm matrix. CsrA acts alternately by repressing GGDEF/EAL encoding proteins which determine c-di-GMP levels , or by favoring motility, rather than biofilm formation, by stabilizing transcripts encoding the master regulator of flagella, FlhDC. Several ncRNAs (OmrA/B, RprA, GcvB, McaS) regulate biofilm by repressing csgD , encoding the CsgD master regulator involved in the production of curli fimbria, cellulose, and c-di-GMP. Other ncRNAs (CsrB/CsrC, McaS) favor biofilm formation by blocking CsrA activity (e.g., in E. coli and Salmonella ) or by positively affecting production of c-di-GMP (Qrr1-4) and expression of exopolysaccharides (e.g., V. cholerae ). To exert their function, many of these sRNAs need to be bound to the RNA-binding chaperone Hfq, which has been reported to also repress biofilm by affecting the expression of the GGDEF protein, HmsT ( Y. pestis ), required to synthesize c-di-GMP. Changes in the levels of c-di-GMP are sensed by the GEMM riboswitch which leads to regulation of organelle biosynthesis that promotes the transformation between motile and sessile lifestyles, where increased c-di-GMP leads to increased biofilm formation and vice versa . The RNases E and G mainly cause the decay of ncRNAs that are involved in the biofilm formation. Degradation of the antitoxin mqsA transcript by the MqsR toxin, leads to inhibition of motility, and induction of csgD , favoring both curli and cellulose production. Environmental factors such as nutrient concentrations (glucose, amino acids) and other physiological stresses (osmolarity, pH, oxidative stress, antimicrobials) are important signals mediating the switch from the planktonic motile to sessile biofilm lifestyles. RNA-binding proteins are shown in orange, ncRNAs are shown in green, riboswitches are shown in pink, TA systems are shown in dark blue and RNases are shown in violet. CsgD, FlhDC, NhaR, and RpoS are major transcriptional regulators. Cellulose, PGA and EPS are expolysaccharides. Hard arrows indicate a direct or indirect positive effect, while truncated arrows indicate a direct or indirect negative effect. Black arrows show those mechanisms that are present in E. coli and are shared in many other pathogens, while red arrows show those mechanism that are present in specific microorganisms (see text for details).

    Article Snippet: Employing ncRNAs to fine-tune the expression of genes, stabilize mRNA, and regulate biofilm formation is an energetically economical strategy (Waters and Storz, ).

    Techniques: RNA Binding Assay, Blocking Assay, Activity Assay, Expressing, Transformation Assay, Inhibition

    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

    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:

    Summary of biofilm impact on the host varying from detrimental to beneficial effects according to the epibiont’s identity, the type of interaction considered and the environmental conditions . Via a recruitment/detachment equilibrium – controlled by environmental and host traits – epibiotic bacterial communities are connected to the free water phase. When forming a biofilm, bacteria experience a boost in activity and interactions. The host will experience a certain reduction in irradiation. Fouling, infections and predation will be affected by the presence of a biofilm, but extent and even sign of these effects are context-specific. An algal host will experience a reduction or an enhancement in nutrient availability depending on whether the autotrophic, respectively heterotrophic components prevail in the biofilm. Wastes and secondary metabolites (including infochemicals) may be metabilized by the biofilm.

    Journal: Frontiers in Microbiology

    Article Title: The Second Skin: Ecological Role of Epibiotic Biofilms on Marine Organisms

    doi: 10.3389/fmicb.2012.00292

    Figure Lengend Snippet: Summary of biofilm impact on the host varying from detrimental to beneficial effects according to the epibiont’s identity, the type of interaction considered and the environmental conditions . Via a recruitment/detachment equilibrium – controlled by environmental and host traits – epibiotic bacterial communities are connected to the free water phase. When forming a biofilm, bacteria experience a boost in activity and interactions. The host will experience a certain reduction in irradiation. Fouling, infections and predation will be affected by the presence of a biofilm, but extent and even sign of these effects are context-specific. An algal host will experience a reduction or an enhancement in nutrient availability depending on whether the autotrophic, respectively heterotrophic components prevail in the biofilm. Wastes and secondary metabolites (including infochemicals) may be metabilized by the biofilm.

    Article Snippet: Quorum sensing and its modulation Quorum sensing is a cell-cell communication mechanism that allows bacteria to coordinate settlement, swarming, reproduction, biofilm formation, stress resistance, dispersal, and production of secondary metabolites (Waters and Bassler, ; Irie and Parsek, ; Steinberg et al., ).

    Techniques: Activity Assay, Irradiation