Journal: The Journal of Biological Chemistry

Article Title: A Novel A3 Group Aconitase Tolerates Oxidation and Nitric Oxide *

doi: 10.1074/jbc.M114.614164

Figure Lengend Snippet: Specific activity of bacterial aconitases

Article Snippet: These results indicate that the AcnA3 activity is resistant to oxidants. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Strain Accession number Specific activity Purified Activated μ mol/min/mg AcnA family α-Proteobacteria O. anthropi ATCC 49188 T Oant_0105 36 ± 3 33 ± 2 S. japonicum UT26S SJA_C1-23180 30 ± 1 26 ± 1 β-Proteobacteria A. denitrificans YD35 AcnA3 107 ± 3 103 ± 4 B. bronchiseptica NBRC 13691 T BB1844 82 ± 3 76 ± 4 D. acidovorans NBRC 14950 T Daci_2441 73 ± 9 69 ± 10 R. eutropha NBRC 102504 H16_A2638 74 ± 3 67 ± 4 γ-Proteobacteria E. coli DH10B ECDH10B_1393 44 ± 3 40 ± 2 P. aeruginosa PAO1 PA1562 40 ± 1 33 ± 2 Methylcitrate dehydratase A. denitrificans YD35 AcnA4 27 ± 2 25 ± 1 D. acidovorans NBRC 14950 T Daci_3587 25 ± 1 26 ± 1 P. aeruginosa PAO1 PA0794 36 ± 1 31 ± 1 R. eutropha NBRC 102504 H16_A1907 33 ± 3 25 ± 1 AcnB family A. denitrificans YD35 AcnB 0.6 ± <0.1 13 ± 0.4 E. coli DH10B ECDH10B_0098 1.4 ± 0.3 3 ± 0.2 P. aeruginosa PAO1 PA1787 1.6 ± 0.2 11 ± 2 R. eutropha NBRC 102504 H16_B0568 0.7 ± 0.1 1.6 ± 0.1 Open in a separate window Specific activity of bacterial aconitases fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIGURE 6. caption a7 Properties of purified AcnA3 and AcnA4.

Techniques: Activity Assay, Purification

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Chemotaxis of Dictyostelium and Acanthamoeba to folate. Chemotaxis assays were set up as described in the methods section. (A) Images of Dictyostelium (Dd) and Acanthamoeba (Ac) 2.5 h after plating with no folate, 10 μM folate, or 100 μM folate. Images are orientated with the folate chemoattractant diffusing from the upper side of the image. Representative images are shown. Each chemotaxis assay typically included the analysis of 6 droplets (minimum of 4) and each assay was repeated at least 2 times. Circles on the image represent the approximate cell droplet perimeter at the time of plating and the horizontal lines bisect the upper and lower halves of the circle. In cases where migrating cells moved beyond a single field of view multiple images were collected to account for all migrating cells. (B) Distance traveled of the leading edge of migrating Dictyostelium (open bars) and Acanthamoeba (black bars) toward the source of folate. Data are the mean distance measured for 6 droplets of cells. For each concentration of folate this chemotaxis assay was repeated 6 times and the data from one representative assay is shown. Unpaired Student’s t-test p values for assays with or without folate were determined (Dictyostelium assays p ⪡ 0.001 and Acanthamoeba assays p > 0.03). (C) Chemotaxis index of Dictyostelium (open bars) and Acanthamoeba (black bars) assayed with folate (10 μM) exposure or without (0 μM). The chemotaxis index was determined by the number of cells outside the original droplet perimeter on the side facing the source of folate divided by the number of cells outside the perimeter facing away from the source of folate. Data is the mean chemotaxis index from 6 droplets of cells. This assay was repeated at least 3 times and data shown represents a typical assay. Error bars represent the standard deviation of the mean. Unpaired Student’s t-test p values for chemotactic index assays with or without folate were determined (Dictyostelium p = 0.0006 and Acanthamoeba p = 1.0).

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Chemotaxis Assay, Concentration Assay, Standard Deviation

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Migration maps of Dictyostelium and Acanthamoeba in folate chemotaxis assays. Time-lapse photography of Dictyostelium (Dd upper image) and Acanthamoeba (Ac lower image) in response to 1 mM folate (source diffusing from the upper side of each image) after approximately 2 h after plating. Only the final image is shown but images were collected every 20 s for 33 min as described in the methods section. Tracks of individual cells were traced using 5 time points (approximately every 6 min) using MTrackplugin in ImageJ and overlaid on the final image. The number for each track is located near the tail of each track. Cells near the leading edge and with relatively few cell-cell interactions were chosen for track analysis. Movies containing all time-lapse images are included in the Supplementary Material Figures S1, S2.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Migration, Chemotaxis Assay

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Chemotaxis of Dictyostelium and Acanthamoeba to bacteria. Chemotaxis assays were set up as described in the methods section. (A) Images of Dictyostelium (Dd) and Acanthamoeba (Ac) 2.5 h after plating with Klebsiella aerogenes, Escherichia coli, and Pseudomonas aeruginosa. Images are orientated with the bacterial source orientated on the upper side of the image. Representative images are shown from an assay that included 6 droplet of either Dictyostelium (Dd) or Acanthamoeba (Ac). Each chemotaxis assay that included a minimum of 4 cell droplets was repeated at least 2 times. Original droplet perimeters and bisector lines were determined as described in Figure 1. In cases where migrating cells moved beyond a single field of view multiple images were collected to account for all migrating cells. (B) Chemotactic index of Dictyostelium (open bars) and Acanthamoeba (black bars) to bacterial droplets. Data is the mean chemotaxis index from 6 droplets of cells. This assay was repeated at least 3 times and data shown represents a typical assay. Error bars represent the standard deviation of the mean. Unpaired Student’s t-test p values for chemotactic index assays with or without bacteria was determined (all Dictyostelium assays p < 0.001 and Acanthamoeba assays *p = 0.6, **p = 0.05, ***p = 0.04).

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Chemotaxis Assay, Bacteria, Standard Deviation

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Migration maps of Dictyostelium and Acanthamoeba in chemotaxis to Klebsiella aerogenes. Time-lapse photography of Dictyostelium (Dd upper image) and Acanthamoeba (Ac lower image) in response to K. aerogenes droplets (positioned on the upper side of each image) after approximately 2 h after plating. Only the final image is shown but images were collected and tracks were traced as described Figure 2. The number for each track is located near the tail of each track. Cells near the leading edge and with relatively few cell-cell interactions were chosen for track analysis. Movies containing all time-lapse images are included in the Supplementary Material Figures S3, S4.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Migration, Chemotaxis Assay

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Percent identity of amoeboid Gα subunits to the Dd Gα4 subunit.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques:

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Phylogenetic tree of Dictyostelium and Acanthamoeba G protein Gα subunits. BLAST searches were used to identify Gα subunit homologs in Dictyostelium discoideum (Dd) and Acanthamoeba castenalli (Ac) genomes. A phylogenetic tree was generated as described in the methods section. The Arabidopsis thaliana Gα subunit (AtGPA1) was used as an out-group. Each sequence has an accession reference number.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Generated, Sequencing

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Phylogenetic trees of G protein Gβ subunits/Racks and Gγ subunits of some amoebozoan and other select eukaryotes. (A) Phylogenetic tree of Gβ and Rack subunit homologs identified through BLAST searches. Only one Gβ subunit of the multiple Gβ subunits from the human (Hs) genome was selected for comparison purposes. (B) Phylogenetic tree of Gγ subunit homologs identified through BLAST searches. Phylogenetic trees were generated as described in the methods section. Species represented include Dictyostelium discoideum (Dd), Acanthamoeba castenalli (Ac), Homo sapien (Hs), Xenopus laevis (Xl), Arabidopsis thaliana (At), Dictyostelium purpureum (Dp), Polysphondylium pallidum (Pp), Dictyostelium fasciculatum (Df), and Saccharomyces cerevisiae (Sc) genomes. Each sequence has an accession reference number.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques: Comparison, Generated, Sequencing

Journal: Protist

Article Title: Acanthamoeba and Dictyostelium Use Different Foraging Strategies

doi: 10.1016/j.protis.2016.08.006

Figure Lengend Snippet: Model of Acanthamoeba movement. Nutrient deprivation primarily results in random motion allowing cells to disperse in all directions (thick dark gray arrows). Movement toward a chemoattractant (thin light gray arrows) is very weak compared to other amoebae such as Dictyostelium.

Article Snippet: The axenic Dictyostelium discoideum strain KAx3 and the Acanthamoeba castellanii strain ATCC 30010 were used in this study.

Techniques:

Journal: Microbial Ecology

Article Title: Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?

doi: 10.1007/s00248-024-02450-8

Figure Lengend Snippet: Examples of patents derived from Paenibacillus spp., aiming at bioprotection against fungal phytopathogens

Article Snippet: Paenibacillus polymyxa strain ATCC 202127 for biocontrol of bacteria and fungi (US6602500) , P. polymyxa ATCC 202127 (= PKB1) , PKB1 antibiotic peptides , Leptosphaeria maculans , Sclerotinia sp., Rhizoctonia sp., Pythium sp., Fusarium spp., Alternaria sp., Aspergillus sp., Sporobolomyces spp., Trichoderma sp., Penicillium sp., Marasmius sp..

Techniques: Derivative Assay, Bacteria, Isolation

Journal: Microbial Ecology

Article Title: Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?

doi: 10.1007/s00248-024-02450-8

Figure Lengend Snippet: Examples of agricultural fungicides derived from Paenibacillus spp., applied in bioprotection against fungal phytopathogens

Article Snippet: Paenibacillus polymyxa strain ATCC 202127 for biocontrol of bacteria and fungi (US6602500) , P. polymyxa ATCC 202127 (= PKB1) , PKB1 antibiotic peptides , Leptosphaeria maculans , Sclerotinia sp., Rhizoctonia sp., Pythium sp., Fusarium spp., Alternaria sp., Aspergillus sp., Sporobolomyces spp., Trichoderma sp., Penicillium sp., Marasmius sp..

Techniques: Derivative Assay, Bacteria

Journal: Microbial Ecology

Article Title: Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?

doi: 10.1007/s00248-024-02450-8

Figure Lengend Snippet: Structural formulae of some non-ribosomally synthesized antimicrobial peptides produced by Paenibacillus strains [ – ]

Article Snippet: Paenibacillus polymyxa strain ATCC 202127 for biocontrol of bacteria and fungi (US6602500) , P. polymyxa ATCC 202127 (= PKB1) , PKB1 antibiotic peptides , Leptosphaeria maculans , Sclerotinia sp., Rhizoctonia sp., Pythium sp., Fusarium spp., Alternaria sp., Aspergillus sp., Sporobolomyces spp., Trichoderma sp., Penicillium sp., Marasmius sp..

Techniques: Synthesized, Produced

Journal: Microbial Ecology

Article Title: Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?

doi: 10.1007/s00248-024-02450-8

Figure Lengend Snippet: Fungistatic activity of Paenibacillus strains; a bacterial strains known to suppress fungal growth; b main antimicrobial mechanisms and their occurrence

Article Snippet: Paenibacillus polymyxa strain ATCC 202127 for biocontrol of bacteria and fungi (US6602500) , P. polymyxa ATCC 202127 (= PKB1) , PKB1 antibiotic peptides , Leptosphaeria maculans , Sclerotinia sp., Rhizoctonia sp., Pythium sp., Fusarium spp., Alternaria sp., Aspergillus sp., Sporobolomyces spp., Trichoderma sp., Penicillium sp., Marasmius sp..

Techniques: Activity Assay

Journal: Microbial Ecology

Article Title: Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?

doi: 10.1007/s00248-024-02450-8

Figure Lengend Snippet: Fungistatic activity of Paenibacillus spp. (antifungal factor unknown)

Article Snippet: Paenibacillus polymyxa strain ATCC 202127 for biocontrol of bacteria and fungi (US6602500) , P. polymyxa ATCC 202127 (= PKB1) , PKB1 antibiotic peptides , Leptosphaeria maculans , Sclerotinia sp., Rhizoctonia sp., Pythium sp., Fusarium spp., Alternaria sp., Aspergillus sp., Sporobolomyces spp., Trichoderma sp., Penicillium sp., Marasmius sp..

Techniques: Activity Assay