Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 1. a) Reported steps involved in the catabolic degradation of camphor by Pseudomonas putida (ATCC 17453). a Chemical structures of (+)-borneol, (L)-glutamic acid, (D)-glutamic acid, and 1-phenylimidazole. 1= (+)-camphor; 2 = 5-exo-hydroxycamphor; 3 = 5-ketocamphor; 4 = unstable lactone; 5 = 2-oxo-Δ3–4,5,5-trimethylcyclopentenylacetic acid; 6 = 2-oxo- Δ3–4,5,5-tri-methylcyclopentenylacetyl-CoA; 7 = 3,4,4-trimethyl-Δ3-pimelyl-CoA; 8 = (+)-borneol; 9 = (L)-glutamicacid; 10 = (D)-glutamic acid; 11 = 1-phe- nylimidazole; A = P450cam, PdR, & PdX; B = 5-exo-hydroxycamphor dehydrogenase; C = 2,5-diketocamphane monooxygenase; D = 2-oxo-Δ3–4,5,5-tri- methylcyclo-pentenylacetyl-CoA synthetase; E = 2-oxo-Δ3–4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques:

Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 2. Effects of1-phenylimidazole (a P450cam inhibitor) on growth P. putida ATCC 17453 (Strain 1). A)Survival dose response of Strain 1treated with 1-phenyli- midazole. B)Growthof Strain 1 on minimal medium with1-phenylimidazole as a sole carbon source. Each point represents the mean ± S. E. of 3 replicates.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques:

Journal: Biochimica et biophysica acta. General subjects

Article Title: Chemotaxis by Pseudomonas putida (ATCC 17453) towards camphor involves cytochrome P450 cam (CYP101A1).

doi: 10.1016/j.bbagen.2018.10.018

Figure Lengend Snippet: Fig. 4. Survival assay with (+)-camphor in the presence and absence of 1-phenylimidazole (a cytochrome P450cam inhibitor).A) Dose response for P. putida ATCC 17453 treated with (+)-camphor. B) Dose response for P. putida ATCC 17453, grown in the presence of 1-phenylimidazole (20 mM) and treated with (+)-camphor. Each point represents the mean ± S. E. of 3 replicates.

Article Snippet: In-plug chemotaxis assays of P. putida strains (ATCC 17453, 17,484, & 33,015) The chemotactic responses of three wild, aerobic,P. putidasoil Strain 2= Pseudomonas putida ATCC 17484 (naphthalene-metabolizing).

Techniques: Clonogenic Cell Survival Assay

Journal: PLoS ONE

Article Title: Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen

doi: 10.1371/journal.pone.0268645

Figure Lengend Snippet: Graphs shown represent survival characteristics of three O157 strains in comparison to E . coli Nal R (#5735), in vitro (A) and in vivo (B), in MRF. Bacterial survival characteristics depicted are following anaerobic incubation for 48 h, in vitro in flasks with MRF or in vivo in the rumen of animals fed the maintenance diet. Viable counts in colony forming units [cfu]/ml, with the standard error of means, are shown in both graphs. Key for each bacterial strain tested is also shown. Inserted tables show pH and VFA composition of MRF used in the in vitro (1A) and in vivo (1B) experiments.

Article Snippet: The four different E . coli strains used in this study included, (i) E . coli Nal R (NADC stock #5735; stx1 -, stx2 -, eae -), a non-pathogenic, nalidixic-resistant derivative of a bovine commensal E . coli , (ii) O157 strain 86–24 ( stx2 +, eae +), a wild-type, human, O157:H7 isolate from an outbreak in Washington State [ , ], (iii) O157 strain EDL933 (ATCC®43895TM; stx1 +, stx2 +, eae +), a wild-type, human, O157:H7 isolate associated with the 1982 multi-state outbreak involving contaminated hamburgers (6), and (iv) O157 strain SS17 ( stx2 +, eae +), a bovine, wild-type, super-shed O157 [ ].

Techniques: Comparison, In Vitro, In Vivo, Incubation

Journal: PLoS ONE

Article Title: Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen

doi: 10.1371/journal.pone.0268645

Figure Lengend Snippet: Graphs shown represent survival characteristics of three O157 strains in comparison to E . coli Nal R (#5735), in vitro (A) and in vivo (B), in LRF. Bacterial survival characteristics depicted are following anaerobic incubation for 48 h, in vitro in flasks with LRF or in vivo in the rumen of animals fed the lactation diet. Viable counts in colony forming units [cfu]/ml, with the standard error of means, are shown in both graphs. Inserted tables show pH and VFA composition of LRF used in the in vitro (2A) and in vivo (2B) experiments.

Article Snippet: The four different E . coli strains used in this study included, (i) E . coli Nal R (NADC stock #5735; stx1 -, stx2 -, eae -), a non-pathogenic, nalidixic-resistant derivative of a bovine commensal E . coli , (ii) O157 strain 86–24 ( stx2 +, eae +), a wild-type, human, O157:H7 isolate from an outbreak in Washington State [ , ], (iii) O157 strain EDL933 (ATCC®43895TM; stx1 +, stx2 +, eae +), a wild-type, human, O157:H7 isolate associated with the 1982 multi-state outbreak involving contaminated hamburgers (6), and (iv) O157 strain SS17 ( stx2 +, eae +), a bovine, wild-type, super-shed O157 [ ].

Techniques: Comparison, In Vitro, In Vivo, Incubation

Journal: PLoS ONE

Article Title: Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen

doi: 10.1371/journal.pone.0268645

Figure Lengend Snippet: iBAQ : A. Venn diagram showing the number of O157 proteins differentially expressed (L2FC >1) between MRF and LRF. B. Venn diagram showing the number of O157 proteins uniquely expressed in MRF and LRF. iTRAQ analysis #1 (reference-based): A. Venn diagram showing number of differentially expressed proteins in the in vitro and in vivo growth conditions, relative to the 86–24 in-vitro proteome, in MRF. B. Venn diagram showing number of differentially expressed proteins in the in vitro and in vivo growth conditions, relative to the 86–24 in-vitro proteome, in LRF.

Article Snippet: The four different E . coli strains used in this study included, (i) E . coli Nal R (NADC stock #5735; stx1 -, stx2 -, eae -), a non-pathogenic, nalidixic-resistant derivative of a bovine commensal E . coli , (ii) O157 strain 86–24 ( stx2 +, eae +), a wild-type, human, O157:H7 isolate from an outbreak in Washington State [ , ], (iii) O157 strain EDL933 (ATCC®43895TM; stx1 +, stx2 +, eae +), a wild-type, human, O157:H7 isolate associated with the 1982 multi-state outbreak involving contaminated hamburgers (6), and (iv) O157 strain SS17 ( stx2 +, eae +), a bovine, wild-type, super-shed O157 [ ].

Techniques: Multiplex sample analysis, In Vitro, In Vivo

Journal: PLoS ONE

Article Title: Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen

doi: 10.1371/journal.pone.0268645

Figure Lengend Snippet: O157 proteins up-regulated, under the in vitro and in vivo growth conditions, in MRF and LRF, as determined by reference-based iTRAQ analysis #1. (Reference:86–24 in vitro proteome).

Article Snippet: The four different E . coli strains used in this study included, (i) E . coli Nal R (NADC stock #5735; stx1 -, stx2 -, eae -), a non-pathogenic, nalidixic-resistant derivative of a bovine commensal E . coli , (ii) O157 strain 86–24 ( stx2 +, eae +), a wild-type, human, O157:H7 isolate from an outbreak in Washington State [ , ], (iii) O157 strain EDL933 (ATCC®43895TM; stx1 +, stx2 +, eae +), a wild-type, human, O157:H7 isolate associated with the 1982 multi-state outbreak involving contaminated hamburgers (6), and (iv) O157 strain SS17 ( stx2 +, eae +), a bovine, wild-type, super-shed O157 [ ].

Techniques: In Vitro, In Vivo, Multiplex sample analysis, Binding Assay, Starch, Membrane, Maltodextrin, Transduction, Clinical Proteomics, Phospho-proteomics, Gene Expression, Chemotaxis Assay, Activity Assay, Ligand Binding Assay, Scaffolding

Journal: PLoS ONE

Article Title: Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen

doi: 10.1371/journal.pone.0268645

Figure Lengend Snippet: The plots depicting the similarity of global protein expression between O157 strains tested in (A) MRF or (B) LRF, in vitro and in vivo . This is based on Bray-Curtis dissimilarities generated from Scaffold normalized iTRAQ reporter intensities generated in reference-free iTRAQ analysis #2.

Article Snippet: The four different E . coli strains used in this study included, (i) E . coli Nal R (NADC stock #5735; stx1 -, stx2 -, eae -), a non-pathogenic, nalidixic-resistant derivative of a bovine commensal E . coli , (ii) O157 strain 86–24 ( stx2 +, eae +), a wild-type, human, O157:H7 isolate from an outbreak in Washington State [ , ], (iii) O157 strain EDL933 (ATCC®43895TM; stx1 +, stx2 +, eae +), a wild-type, human, O157:H7 isolate associated with the 1982 multi-state outbreak involving contaminated hamburgers (6), and (iv) O157 strain SS17 ( stx2 +, eae +), a bovine, wild-type, super-shed O157 [ ].

Techniques: Expressing, In Vitro, In Vivo, Generated, Multiplex sample analysis

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Comparison of predicted amino acid sequences for FimAs encoded by the fimA genes of various P. gingivalis strains and type V fimA gene. Amino acid identities are shown by asterisks. Hyphens are used to indicate the positions of gaps in the multiple alignment. The putative signal peptides are underlined. The number of amino acids and the molecular weight of the FimA of each strain are given. The alignment of the deduced amino acid sequences was performed with the CLUSTAL W program of the DNA Data Bank of Japan.

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques: Comparison, Molecular Weight

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Evolutionary relationships based on synonymous site variation in the fimA gene of P. gingivalis. The neighbor-joining method was used to construct the phylogenetic tree, using CLUSTAL W (DNA Data Bank of Japan) and TreeView software (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html).

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques: Construct, Software

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Distribution of P. gingivalis with type I to V fimA in 73 clinical samples from periodontitis patients

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques:

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Southern blot analyses of P. gingivalis specific genes. Genomic DNA was isolated from each strain; digested with EcoRI, BamHI, and HindIII; and then separated on a 1% agarose gel. After blotting to a nylon membrane, P. gingivalis specific genes were probed with 32P-labeled fimA, sod, and kgp gene fragments from strain ATCC 33277. Lanes: 1, ATCC 33277; 2, HW24D1; 3, 6/26; 4, HG564; 5, HNA-99.

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques: Southern Blot, Isolation, Agarose Gel Electrophoresis, Membrane, Labeling

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Western blot analyses of the FimAs in five type-representative strains of P. gingivalis. Whole-cell lysates of P. gingivalis (2 × 107 cells) were separated by SDS–12% polyacrylamide gel electrophoresis. After electrophoresis, gels were transferred to polyvinylidene difluoride membranes and FimA was detected with antibodies to rFimA (381, type I fimA [A], and HG564, type IV fimA [B]). Lanes: M, prestained protein marker; 1, P. gingivalis ATCC 33277; 2, P. gingivalis HW24D1; 3, P. gingivalis 6/26; 4, P. gingivalis HG564; 5, P. gingivalis HNA-99. Arrows indicate FimA.

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques: Western Blot, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker

Journal:

Article Title: Distribution and Molecular Characterization of Porphyromonas gingivalis Carrying a New Type of fimA Gene

doi:

Figure Lengend Snippet: Binding of P. gingivalis representing the five different fimA types to HA and sHA beads. Three milligrams of HA beads equilibrated with buffered KCl or clarified whole human saliva was added to a siliconized borosilicate tube and incubated with different numbers of the 3H-labeled P. gingivalis (106 to 108) cells in a total volume of 300 μl with a gentle, oscillating motion for 1 h at room temperature. The mixture was layered on 100% Percoll to separate unbound cells from the bead-bound cells. After washing, radioactivity of the bead-bound cells was quantitated with a liquid scintillation counter. The results are shown as the mean values of triplicate samples from three individual experiments. One-way analysis of variance and the Tukey-Kramer test were used for the comparison of the binding abilities of P. gingivalis cells (∗, P < 0.0001).

Article Snippet: The multiple alignment analysis showed that this gene fragment has sequence homology with type I fimA (strain ATCC 33277) (49%), type II fimA (strain HW24D1) (49%), type III fimA (strain 6/26) (52%), and type IV fimA (strain HG564) (59%).

Techniques: Binding Assay, Incubation, Labeling, Gentle, Radioactivity, Comparison