Journal: PLoS ONE

Article Title: Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

doi: 10.1371/journal.pone.0051931

Figure Lengend Snippet: Expected bacterial 16S rRNA gene copies were calculated based on four and five 16S copies per genome for ( a ) P. aeruginosa and ( b ) D. vulgaris , respectively. Black bars = predicted 16S copies. White bars = estimated 16S copies based on supercoiled plasmid standard. Grey bars = estimated 16S copies based on nicked-circular plasmid standard. Black and white striped bars = estimated 16S copies based on linearized plasmid standard. Black and gray striped bars = estimated 16S copies based on amplicon-based standard. Data are the average (n = 3) and error bars are ±1 standard deviation among replicates.

Article Snippet: Lyophilized genomic DNA samples from Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough (NCIB 8303/ATCC 29579), Pseudomonas aeruginosa strain PAO1-LAC (ATCC 47085), Archaeoglobus fulgidus strain VC16 (DSM 4304/ATCC 49203), and Methanocaldococcus jannaschii strain JAL-1 (DSM 2661/ATCC 43067) were purchased from the American Type Culture Collection (ATCC).

Techniques: Plasmid Preparation, Amplification, Standard Deviation

Journal: PLoS ONE

Article Title: Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

doi: 10.1371/journal.pone.0051931

Figure Lengend Snippet: Estimated and expected 16S rRNA gene copies in microbial gDNA samples based on qPCR standard curves.

Article Snippet: Lyophilized genomic DNA samples from Desulfovibrio vulgaris subsp. vulgaris strain Hildenborough (NCIB 8303/ATCC 29579), Pseudomonas aeruginosa strain PAO1-LAC (ATCC 47085), Archaeoglobus fulgidus strain VC16 (DSM 4304/ATCC 49203), and Methanocaldococcus jannaschii strain JAL-1 (DSM 2661/ATCC 43067) were purchased from the American Type Culture Collection (ATCC).

Techniques: Amplification

Journal: Scientific Reports

Article Title: The bacterial Mrp ORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis

doi: 10.1038/s41598-018-37021-8

Figure Lengend Snippet: Unrooted Maximum likelihood tree of the Mrp/Nbp35 ATP-binding protein family (IPR019591, 16154 sequences, 114 amino acid positions conserved for the analysis after trimming). The tree is displayed as a cladogramme. Branch colors correspond to taxonomic groups: pink = Bacteria , blue = Eucarya , green = Archaea . DVU2109, DVU1847, and DVU2330 from Desulfovibrio vulgaris strain Hildenborough ATCC 29579, Dde3202 from Desulfovibrio alaskensis strain G20, Mrp from Escherichia coli strain K12, ApbC from Salmonella typhimurium strain LT2 SGSC1412 ATCC 700720, Cfd1 and Nbp35 from Saccharomyces cerevisiae strain ATCC 204508 S288c are indicated by red triangles. The 99 sequences associating a P-loop NTPase domain and a Di-Nase domain are indicated by purple triangles. Because of the large number of sequences contained in the tree, some triangles may overlap.

Article Snippet: DVU2109, DVU1847, and DVU2330 from Desulfovibrio vulgaris strain Hildenborough ATCC 29579, Dde3202 from Desulfovibrio alaskensis strain G20, Mrp from Escherichia coli strain K12, ApbC from Salmonella typhimurium strain LT2 SGSC1412 ATCC 700720, Cfd1 and Nbp35 from Saccharomyces cerevisiae strain ATCC 204508 S288c are indicated by red triangles.

Techniques: Binding Assay

Journal: Applied and Environmental Microbiology

Article Title: Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

doi: 10.1128/AEM.00691-10

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: Prospect, IL). table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Genotype or relevant characteristics b Source and/or reference E. coli strains TOP10 (both chemically competent and electrocompetent) F − mcrA Δ( mrr - hsdRMS - mcrBC ) φ80 lacZ ΔM15 Δ lacX74 recA1 araD139 Δ( ara - leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen (catalog no. C4040-10 and C4040-50) α-Select (Bronze efficiency) F − deoR end A1 rec A1 rel A1 gyr A96 hsd R17 ( r k − m k + ) pho A supE44 thi -1 Δ( lac ZYA - arg F ) U169 φ80δ lac Z ΔM15 λ − Bioline GM272 F − fhuA2 or fhuA31 , lacY1 or lacZ4 , tsx-1 or tsx-78 , glnV44 (AS) galK2 (Oc) λ− dcm-6 dam-3 mtlA2 metB1 thi-1 ? hsdS21 CGSC a (no. 6478); 17 D. vulgaris strains ATCC 29579 WT D. vulgaris Hildenborough ATCC JW801 WT ΔpDV1 37 JW9021 WT Δ( qmoABC -DVU0851) Km r This study JW9063 WT ΔDVU0851 Km r This study Plasmids pCR8/GW/TOPO TOPO cloning vector; Sp r Invitrogen pCR-XL-TOPO TOPO cloning vector; Km r Invitrogen pSC27 Desulfovibrio shuttle vector; source of aph(3 ′ )-II ; Km r 34 pMO719 pCR8/GW/TOPO containing SRB replicon (pBG1); Sp r 18 pMO9020 pCR8/GW/TOPO with 977 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete qmoABC- DVU0851; Sp r Km r This study pMO9021 pCR-XL-TOPO containing aph(3 ′ )-IIp :: qmoABC -DVU0851; Km r This study pMO9040 pMO719 with aph(3 ′ )-IIp :: qmoABC ; Sp r This study pMO9042 pMO719 with aph(3 ′ )-IIp :: qmoABC- DVU0851; Sp r This study pMO9062 pCR8/GW/TOPO with 964 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete DVU0851; Km r Sp r This study pMO9070 pCR8/GW/TOPO; Km r Sp r This study pMO9071 pMO719 with aph(3 ′ )-II ; Km r Sp r This study pMO9072 pMO719 with aph(3 ′ )-IIp and MCS; Sp r ; for complementation constructs This study pMO9074 pMO9072 with DVU0851 in MCS; Sp r This study pMO9116 pMO9040 with aph(3 ′ )-IIp ::RBS:: qmoABC ; Sp r This study pMO9117 pMO9042 with aph(3 ′ )-IIp ::RBS:: qmoABC -DVU0851; Sp r This study pMO9118 pMO9074 with aph(3 ′ )-IIp ::RBS::DVU0851; Sp r This study Open in a separate window a CGSC, Coli Genetic Stock Center. b WT, wild type; aph(3 ′ )-IIp , promoter from kanamycin resistance gene aph(3 ′ )-II ; MCS, multicloning site; RBS, ribosomal binding site (TGCAGTCCC AGGAGG TACCAT).

Techniques: Plasmid Preparation, Acetylene Reduction Assay, Clone Assay, Construct

Journal: Applied and Environmental Microbiology

Article Title: Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

doi: 10.1128/AEM.00691-10

Figure Lengend Snippet: Growth of D. vulgaris and two deletion mutants on sulfate- and sulfite-containing media. Growth comparisons of D. vulgaris Hildenborough (wild type) and deletion constructs JW9021 [Δ(qmoABC-DVU0851)] and JW9063 (ΔDVU0851) on lactate-sulfate (60 mM-30 mM) (A), lactate-sulfite (60 mM-40 mM) (B), pyruvate-sulfate (60 mM-30 mM) (C), and pyruvate-sulfite (60 mM-40 mM) (D) media are shown. Wild type, white circles; JW9021, black circles; JW9063, gray circles. Readings reflect averages of three samples, and error bars show standard deviations.

Article Snippet: Prospect, IL). table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Genotype or relevant characteristics b Source and/or reference E. coli strains TOP10 (both chemically competent and electrocompetent) F − mcrA Δ( mrr - hsdRMS - mcrBC ) φ80 lacZ ΔM15 Δ lacX74 recA1 araD139 Δ( ara - leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen (catalog no. C4040-10 and C4040-50) α-Select (Bronze efficiency) F − deoR end A1 rec A1 rel A1 gyr A96 hsd R17 ( r k − m k + ) pho A supE44 thi -1 Δ( lac ZYA - arg F ) U169 φ80δ lac Z ΔM15 λ − Bioline GM272 F − fhuA2 or fhuA31 , lacY1 or lacZ4 , tsx-1 or tsx-78 , glnV44 (AS) galK2 (Oc) λ− dcm-6 dam-3 mtlA2 metB1 thi-1 ? hsdS21 CGSC a (no. 6478); 17 D. vulgaris strains ATCC 29579 WT D. vulgaris Hildenborough ATCC JW801 WT ΔpDV1 37 JW9021 WT Δ( qmoABC -DVU0851) Km r This study JW9063 WT ΔDVU0851 Km r This study Plasmids pCR8/GW/TOPO TOPO cloning vector; Sp r Invitrogen pCR-XL-TOPO TOPO cloning vector; Km r Invitrogen pSC27 Desulfovibrio shuttle vector; source of aph(3 ′ )-II ; Km r 34 pMO719 pCR8/GW/TOPO containing SRB replicon (pBG1); Sp r 18 pMO9020 pCR8/GW/TOPO with 977 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete qmoABC- DVU0851; Sp r Km r This study pMO9021 pCR-XL-TOPO containing aph(3 ′ )-IIp :: qmoABC -DVU0851; Km r This study pMO9040 pMO719 with aph(3 ′ )-IIp :: qmoABC ; Sp r This study pMO9042 pMO719 with aph(3 ′ )-IIp :: qmoABC- DVU0851; Sp r This study pMO9062 pCR8/GW/TOPO with 964 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete DVU0851; Km r Sp r This study pMO9070 pCR8/GW/TOPO; Km r Sp r This study pMO9071 pMO719 with aph(3 ′ )-II ; Km r Sp r This study pMO9072 pMO719 with aph(3 ′ )-IIp and MCS; Sp r ; for complementation constructs This study pMO9074 pMO9072 with DVU0851 in MCS; Sp r This study pMO9116 pMO9040 with aph(3 ′ )-IIp ::RBS:: qmoABC ; Sp r This study pMO9117 pMO9042 with aph(3 ′ )-IIp ::RBS:: qmoABC -DVU0851; Sp r This study pMO9118 pMO9074 with aph(3 ′ )-IIp ::RBS::DVU0851; Sp r This study Open in a separate window a CGSC, Coli Genetic Stock Center. b WT, wild type; aph(3 ′ )-IIp , promoter from kanamycin resistance gene aph(3 ′ )-II ; MCS, multicloning site; RBS, ribosomal binding site (TGCAGTCCC AGGAGG TACCAT).

Techniques: Construct

Journal: Applied and Environmental Microbiology

Article Title: Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

doi: 10.1128/AEM.00691-10

Figure Lengend Snippet: Dissolved sulfide generated by wild-type D. vulgaris , mutants, and complemented mutants when grown on lactate-sulfate or lactate-sulfite medium a

Article Snippet: Prospect, IL). table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Genotype or relevant characteristics b Source and/or reference E. coli strains TOP10 (both chemically competent and electrocompetent) F − mcrA Δ( mrr - hsdRMS - mcrBC ) φ80 lacZ ΔM15 Δ lacX74 recA1 araD139 Δ( ara - leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen (catalog no. C4040-10 and C4040-50) α-Select (Bronze efficiency) F − deoR end A1 rec A1 rel A1 gyr A96 hsd R17 ( r k − m k + ) pho A supE44 thi -1 Δ( lac ZYA - arg F ) U169 φ80δ lac Z ΔM15 λ − Bioline GM272 F − fhuA2 or fhuA31 , lacY1 or lacZ4 , tsx-1 or tsx-78 , glnV44 (AS) galK2 (Oc) λ− dcm-6 dam-3 mtlA2 metB1 thi-1 ? hsdS21 CGSC a (no. 6478); 17 D. vulgaris strains ATCC 29579 WT D. vulgaris Hildenborough ATCC JW801 WT ΔpDV1 37 JW9021 WT Δ( qmoABC -DVU0851) Km r This study JW9063 WT ΔDVU0851 Km r This study Plasmids pCR8/GW/TOPO TOPO cloning vector; Sp r Invitrogen pCR-XL-TOPO TOPO cloning vector; Km r Invitrogen pSC27 Desulfovibrio shuttle vector; source of aph(3 ′ )-II ; Km r 34 pMO719 pCR8/GW/TOPO containing SRB replicon (pBG1); Sp r 18 pMO9020 pCR8/GW/TOPO with 977 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete qmoABC- DVU0851; Sp r Km r This study pMO9021 pCR-XL-TOPO containing aph(3 ′ )-IIp :: qmoABC -DVU0851; Km r This study pMO9040 pMO719 with aph(3 ′ )-IIp :: qmoABC ; Sp r This study pMO9042 pMO719 with aph(3 ′ )-IIp :: qmoABC- DVU0851; Sp r This study pMO9062 pCR8/GW/TOPO with 964 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete DVU0851; Km r Sp r This study pMO9070 pCR8/GW/TOPO; Km r Sp r This study pMO9071 pMO719 with aph(3 ′ )-II ; Km r Sp r This study pMO9072 pMO719 with aph(3 ′ )-IIp and MCS; Sp r ; for complementation constructs This study pMO9074 pMO9072 with DVU0851 in MCS; Sp r This study pMO9116 pMO9040 with aph(3 ′ )-IIp ::RBS:: qmoABC ; Sp r This study pMO9117 pMO9042 with aph(3 ′ )-IIp ::RBS:: qmoABC -DVU0851; Sp r This study pMO9118 pMO9074 with aph(3 ′ )-IIp ::RBS::DVU0851; Sp r This study Open in a separate window a CGSC, Coli Genetic Stock Center. b WT, wild type; aph(3 ′ )-IIp , promoter from kanamycin resistance gene aph(3 ′ )-II ; MCS, multicloning site; RBS, ribosomal binding site (TGCAGTCCC AGGAGG TACCAT).

Techniques: Generated, Plasmid Preparation

Journal: Applied and Environmental Microbiology

Article Title: Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

doi: 10.1128/AEM.00691-10

Figure Lengend Snippet: Growth of D. vulgaris deletion and complementation strains on sulfate-containing media. (A) Growth of wild-type D. vulgaris (white circles), JW9021 [Δ(qmoABC-DVU0851)] (black circles), and three complemented strains, JW9021(pMO9116) [Δ(qmoABC-DVU0851)] complemented with qmoABC (white squares), JW9021(pMO9117) [Δ(qmoABC-DVU0851)] complemented with qmoABC-DVU0851 (black squares), and JW9021(pMO9118) [Δ(qmoABC-DVU0851)] complemented with DVU0851 (gray squares), on defined lactate-sulfate (60 mM-30 mM) medium. (B) Growth of these strains on defined pyruvate-sulfate (60 mM-30 mM) medium. (C) Growth of wild-type D. vulgaris (white circles), JW9063 (ΔDVU0851) (gray circles), and JW9063(pMO9118) (ΔDVU0851) complemented with DVU0851 (▵) on defined lactate-sulfate medium. Optical density readings are averages of three samples, and error bars show standard deviations.

Article Snippet: Prospect, IL). table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Genotype or relevant characteristics b Source and/or reference E. coli strains TOP10 (both chemically competent and electrocompetent) F − mcrA Δ( mrr - hsdRMS - mcrBC ) φ80 lacZ ΔM15 Δ lacX74 recA1 araD139 Δ( ara - leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen (catalog no. C4040-10 and C4040-50) α-Select (Bronze efficiency) F − deoR end A1 rec A1 rel A1 gyr A96 hsd R17 ( r k − m k + ) pho A supE44 thi -1 Δ( lac ZYA - arg F ) U169 φ80δ lac Z ΔM15 λ − Bioline GM272 F − fhuA2 or fhuA31 , lacY1 or lacZ4 , tsx-1 or tsx-78 , glnV44 (AS) galK2 (Oc) λ− dcm-6 dam-3 mtlA2 metB1 thi-1 ? hsdS21 CGSC a (no. 6478); 17 D. vulgaris strains ATCC 29579 WT D. vulgaris Hildenborough ATCC JW801 WT ΔpDV1 37 JW9021 WT Δ( qmoABC -DVU0851) Km r This study JW9063 WT ΔDVU0851 Km r This study Plasmids pCR8/GW/TOPO TOPO cloning vector; Sp r Invitrogen pCR-XL-TOPO TOPO cloning vector; Km r Invitrogen pSC27 Desulfovibrio shuttle vector; source of aph(3 ′ )-II ; Km r 34 pMO719 pCR8/GW/TOPO containing SRB replicon (pBG1); Sp r 18 pMO9020 pCR8/GW/TOPO with 977 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete qmoABC- DVU0851; Sp r Km r This study pMO9021 pCR-XL-TOPO containing aph(3 ′ )-IIp :: qmoABC -DVU0851; Km r This study pMO9040 pMO719 with aph(3 ′ )-IIp :: qmoABC ; Sp r This study pMO9042 pMO719 with aph(3 ′ )-IIp :: qmoABC- DVU0851; Sp r This study pMO9062 pCR8/GW/TOPO with 964 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete DVU0851; Km r Sp r This study pMO9070 pCR8/GW/TOPO; Km r Sp r This study pMO9071 pMO719 with aph(3 ′ )-II ; Km r Sp r This study pMO9072 pMO719 with aph(3 ′ )-IIp and MCS; Sp r ; for complementation constructs This study pMO9074 pMO9072 with DVU0851 in MCS; Sp r This study pMO9116 pMO9040 with aph(3 ′ )-IIp ::RBS:: qmoABC ; Sp r This study pMO9117 pMO9042 with aph(3 ′ )-IIp ::RBS:: qmoABC -DVU0851; Sp r This study pMO9118 pMO9074 with aph(3 ′ )-IIp ::RBS::DVU0851; Sp r This study Open in a separate window a CGSC, Coli Genetic Stock Center. b WT, wild type; aph(3 ′ )-IIp , promoter from kanamycin resistance gene aph(3 ′ )-II ; MCS, multicloning site; RBS, ribosomal binding site (TGCAGTCCC AGGAGG TACCAT).

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough

doi: 10.1128/AEM.00691-10

Figure Lengend Snippet: Northern blot of D. vulgaris and the Δ(qmoABC-DVU0851) mutant probed for apsA-containing transcript. Determination of apsA-containing transcript from RNA samples of D. vulgaris (lanes 1, 2, 4, and 5) and deletion mutant JW9021 [Δ(qmoABC-DVU0851)] (lanes 3 and 6) grown on lactate-sulfate (60 mM-30 mM) (lanes 1 and 4) or lactate-sulfite (60 mM-40 mM) (lanes 2, 3, 5, and 6) medium. The RNA was probed with an internal fragment of apsA. The agarose gel (lanes 4 to 7) and developed film (lanes 1 to 3) are shown. An RNA ladder (Promega) was also included (lane 7).

Article Snippet: Prospect, IL). table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Genotype or relevant characteristics b Source and/or reference E. coli strains TOP10 (both chemically competent and electrocompetent) F − mcrA Δ( mrr - hsdRMS - mcrBC ) φ80 lacZ ΔM15 Δ lacX74 recA1 araD139 Δ( ara - leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen (catalog no. C4040-10 and C4040-50) α-Select (Bronze efficiency) F − deoR end A1 rec A1 rel A1 gyr A96 hsd R17 ( r k − m k + ) pho A supE44 thi -1 Δ( lac ZYA - arg F ) U169 φ80δ lac Z ΔM15 λ − Bioline GM272 F − fhuA2 or fhuA31 , lacY1 or lacZ4 , tsx-1 or tsx-78 , glnV44 (AS) galK2 (Oc) λ− dcm-6 dam-3 mtlA2 metB1 thi-1 ? hsdS21 CGSC a (no. 6478); 17 D. vulgaris strains ATCC 29579 WT D. vulgaris Hildenborough ATCC JW801 WT ΔpDV1 37 JW9021 WT Δ( qmoABC -DVU0851) Km r This study JW9063 WT ΔDVU0851 Km r This study Plasmids pCR8/GW/TOPO TOPO cloning vector; Sp r Invitrogen pCR-XL-TOPO TOPO cloning vector; Km r Invitrogen pSC27 Desulfovibrio shuttle vector; source of aph(3 ′ )-II ; Km r 34 pMO719 pCR8/GW/TOPO containing SRB replicon (pBG1); Sp r 18 pMO9020 pCR8/GW/TOPO with 977 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete qmoABC- DVU0851; Sp r Km r This study pMO9021 pCR-XL-TOPO containing aph(3 ′ )-IIp :: qmoABC -DVU0851; Km r This study pMO9040 pMO719 with aph(3 ′ )-IIp :: qmoABC ; Sp r This study pMO9042 pMO719 with aph(3 ′ )-IIp :: qmoABC- DVU0851; Sp r This study pMO9062 pCR8/GW/TOPO with 964 bp upstream and 951 bp downstream of aph(3 ′ )-II cassette to delete DVU0851; Km r Sp r This study pMO9070 pCR8/GW/TOPO; Km r Sp r This study pMO9071 pMO719 with aph(3 ′ )-II ; Km r Sp r This study pMO9072 pMO719 with aph(3 ′ )-IIp and MCS; Sp r ; for complementation constructs This study pMO9074 pMO9072 with DVU0851 in MCS; Sp r This study pMO9116 pMO9040 with aph(3 ′ )-IIp ::RBS:: qmoABC ; Sp r This study pMO9117 pMO9042 with aph(3 ′ )-IIp ::RBS:: qmoABC -DVU0851; Sp r This study pMO9118 pMO9074 with aph(3 ′ )-IIp ::RBS::DVU0851; Sp r This study Open in a separate window a CGSC, Coli Genetic Stock Center. b WT, wild type; aph(3 ′ )-IIp , promoter from kanamycin resistance gene aph(3 ′ )-II ; MCS, multicloning site; RBS, ribosomal binding site (TGCAGTCCC AGGAGG TACCAT).

Techniques: Northern Blot, Mutagenesis, Agarose Gel Electrophoresis