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  • 99
    Thermo Fisher nunc f96 microwell polystyrene plate
    Nunc F96 Microwell Polystyrene Plate, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 118 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 118 article reviews
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    Millipore nunc immuno microwell 96 well solid plates
    Nunc Immuno Microwell 96 Well Solid Plates, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher nunc microwell 96 well optical bottom plates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc Microwell 96 Well Optical Bottom Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 393 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher nunc microwell 96 well microplates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc Microwell 96 Well Microplates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 414 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher nunc 96 well polystyrene round bottom microwell plates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc 96 Well Polystyrene Round Bottom Microwell Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher nunc 96 well polystyrene conical bottom microwell plates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc 96 Well Polystyrene Conical Bottom Microwell Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher nunc microwell plates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc Microwell Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore nunc microwell 96 well polystyrene plate
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc Microwell 96 Well Polystyrene Plate, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher nunc 96 well polypropylene microwell plates
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc 96 Well Polypropylene Microwell Plates, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher nunc f96 microwell black and white polystyrene plate
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
    Nunc F96 Microwell Black And White Polystyrene Plate, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore 96 well
    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
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    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.
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    High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to   Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see   STAR Methods ). (B) Alteration of the growth of  Plectosphaerella cucumerina isolate 10  upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( >  97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see   Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.

    Journal: Cell

    Article Title: Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

    doi: 10.1016/j.cell.2018.10.020

    Figure Lengend Snippet: High-Throughput Fungal-Bacterial Interaction Screen and Biocontrol Activities of Bacterial Root Commensals, Related to Figure 5 (A) Schematic overview of the experimental protocol. Fungal spores were equally distributed to the wells of a transparent-bottom 96 well plate and incubated in the presence or absence of different root-derived bacteria (stationary phase) in liquid medium (screening plate). Bacteria were also grown in the absence of fungal spores as a control (background plate). After 48 hours of interaction, three washing steps were used to eliminate bacterial cells in suspension. Note that the fungal mycelium sticks to the transparent optical bottom of the plate. After overnight incubation in Wheat Germ Agglutinin and two additional washes, the fluorescence intensity (reflecting fungal growth) was measured using a plate reader. The relative growth index was calculated as illustrated (see STAR Methods ). (B) Alteration of the growth of Plectosphaerella cucumerina isolate 10 upon competition with phylogenetically diverse members of the bacterial root microbiota in minimum medium (M9) and a carbon-rich medium (20% TSB). The phylogenetic tree was constructed based on the full bacterial 16S rRNA gene sequences and bootstrap values are depicted with black circles. The heatmap depicts the log2 fungal relative growth index (presence versus absence of bacterial competitors) measured by fluorescence (see above). Note the similar overall inhibitory activities in minimum and complex media. (C) Validation experiment, in which the bacterial strains were re-screened against ten randomly-selected fungi. Fluorescence intensities (log2) were compared with those obtained from the first biological replicate. (D) Comparison of network-derived correlations and experimentally tested interactions of bacterial families with fungal species. For each bacterial family shared between antagonistic screening and root-associated OTU network analysis, the average antagonistic activity against fungal isolates and the cumulative correlation to fungal OTUs in the network are represented. Bacterial families with more than two members were considered and values for both measurements were normalized to be in the same range. (E) Direct comparison of bacterial OTUs from the root network with bacterial isolates used in the antagonistic screening. Each data point corresponds to a bacterial OTU-isolate pair ( > 97% sequence similarity; only best matching hits are shown). For each pair, the network-derived correlation with fungal OTUs (from the bacterial OTU) is plotted against the result from the antagonistic screening (from the bacterial isolates). (F) Same as E) but data are presented in a correlation plot. (G) Validation of withdrawal of a subset of bacterial strains in the FlowPot microbiota reconstitution system. Relative abundances of isolates of the Pseudomonadaceae (top) and the Comamonadaceae (bottom) families in output matrix and root samples four weeks after inoculation (direct mapping at 100% sequence similarity). RA: Relative abundance. -C: withdrawal of ten Comamonadaceae strains, -P: withdrawal of eight Pseudomonadaceae strains. -C-P removal of 18 Comamonadaceae plus Pseudomonadaceae strains. Control samples were inoculated with the full 148-member bacterial community. Note that one Acidovorax strain (Acidovorax 275) was unintentionally not removed from the -C depleted samples. This Acidovorax strain is unable to rescue plant growth in the presence of the fungal community (see Figure 5 C). (H and I) Relative abundance of (H) fungal isolates and (I) bacterial isolates (direct mapping at 100% sequence similarity) is presented for all conditions. B: full 148-member bacterial community. F: 34-member fungal community. -C: depletion of Comamonadaceae isolates. -P: depletion of Pseudomonadaceae isolates. -C-P: depletion of Comamonadaceae and Pseudomonadaceae isolates.

    Article Snippet: Two 96-well optical bottom plates (ThermoFisher Scientific/Nunc, Rochester, USA) were used for the screening.

    Techniques: High Throughput Screening Assay, Incubation, Derivative Assay, Fluorescence, Construct, Activity Assay, Sequencing