Journal:

Article Title: Analysis of dofA , a fruA -Dependent Developmental Gene, and Its Homologue, dofB , in Myxococcus xanthus

doi: 10.1128/JB.184.24.6803-6810.2002

Figure Lengend Snippet: Bacterial strains and plasmids used in this study

Article Snippet: pGEM-T easy , Ap r lacZ cloning vector , Promega.

Techniques: Plasmid Preparation, Clone Assay

Journal:

Article Title: Burkholderia pseudomallei Class A ?-Lactamase Mutations That Confer Selective Resistance against Ceftazidime or Clavulanic Acid Inhibition

doi: 10.1128/AAC.47.7.2082-2087.2003

Figure Lengend Snippet: Bacterial strains and plasmids used in this study

Article Snippet: When used, antibiotics were added at the indicated concentrations. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Description Reference or source Strains E. coli TOP10 F − mcrA Δ( mrr-hsdRMS-mcrBC ) φ80 lacZ ΔM15 Δ lacX 74 deoR recA1 araD139 Δ( ara-leu ) 7697 galU galK rpsL (Str r ) endA1 nupG Invitrogen E. coli BL21 (DE3) F − ompT hsdS B (r B − m B − ) gal dcm (DE3) pLysS (Cam r ) Invitrogen E. coli BL21 (DE3)pLysS BL21(DE3)pLysS: F − ompT hsdS B (r B − m B − ) gal dcm (DE3) pLysS (Cam r ) Invitrogen B. cepacia K56-2 CF isolate, Toronto, Canada 8 B. mallet ATCC 23344 Type strain (human isolate) USAMRIID a B. pseudomallei 316a Clinical isolate, wild-type phenotype 8 B. pseudomallei 316c Clinical isolate, selectively resistant to ceftazidime 8 B. pseudomallei 365c Clinical isolate, wild-type phenotype 8 B. pseudomallei 365a Clinical isolate, derepressed phenotype 8 B. pseudomallei 392a Clinical isolate, wild-type phenotype 8 B. pseudomallei 392f Clinical isolate, decreased susceptibility to clavulanic acid inhibition 8 B. thailandensis ATCC 700388 Type strain (soil isolate) 16 Plasmids pCR2.1-TOPO Topoisomerase-mediated cloning vector: Ap r Km r Invitrogen pEM7/Zeo Expression vector, Zeo r Invitrogen pUCP31T Broad-host-range vector.

Techniques: Plasmid Preparation, Inhibition, Cloning, Expressing, Clone Assay

Journal:

Article Title: Apyrase, the Product of the Virulence Plasmid-Encoded phoN2 ( apy ) Gene of Shigella flexneri , Is Necessary for Proper Unipolar IcsA Localization and for Efficient Intercellular Spread †

doi: 10.1128/JB.188.4.1620-1627.2006

Figure Lengend Snippet: Bacterial strains and plasmids a

Article Snippet: The locations of 3× FLAG-tagged OspB recombinant protein as well as of IpaB, IpaC, and apyrase proteins are indicated. na, not added. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Relevant genotype or characteristic(s) Source or reference Strains M90T Wild-type S. flexneri serotype 5a 32 HND115 M90T Δ phoN2 ; susceptible This work HND201 M90T Δ ospB ; susceptible This work HND215 M90T Δ ospBphoN2 ; susceptible This work HND43 M90T Δ mxiA ; susceptible This work HND53 M90T Δ virB :: aphA-3 ; Km r This work HND549 M90T ospB -3×FLAG; susceptible This work HND5311 M90T Δ mxiA ospB -3×FLAG; susceptible This work SC560 M90T Δ icsA ::Ω; Sm r 10 M15[pREP4] E. coli K-12 strain carrying plasmid pREP4 Qiagen Plasmids pGEM-T Cloning vector, Ap r Promega pBluescript SK Cloning vector, Ap r Stratagene Inc., La Jolla, CA pBAD28 Arabinose-inducible P BAD expression vector, Ap r Cm r 13 pSUB11 Template plasmid carrying a 3×FLAG epitope and Km r cassette 42 pKD46 λ Red helper plasmid; oriR101 repA101 (Ts) P-araB-gam-bet-exo Ap r 7 pKD4 Template plasmid carrying a Km r gene with FLP recognition target sequence 7 pCP20 FLP helper plasmid; pSC101 replicon (Ts) bla cat Flp (λR p ) cI 857 Ap r Cm r 7 pREP4 lacI , Km r Qiagen pQE30 Cloning vector; Ap r Qiagen pHN301 pQE30 carrying His6- phoN2 ; Ap r This work pHN28 pBAD28 carrying phoN2 ; Ap r Cm r This work pHN111 pBAD28 carrying mxiA ; Ap r Cm r This work pFB1-4 pBluescript SK carrying a mutated phoN2 gene of EIEC strain HN280 presenting the R192P amino acid substitution 36 Open in a separate window a Ap r , ampicillin resistance; Cm r , cloramphenicol resistance; Km r , kanamycin resistance.

Techniques: Plasmid Preparation, Clone Assay, Expressing, Sequencing

Journal:

Article Title: Apyrase, the Product of the Virulence Plasmid-Encoded phoN2 ( apy ) Gene of Shigella flexneri , Is Necessary for Proper Unipolar IcsA Localization and for Efficient Intercellular Spread †

doi: 10.1128/JB.188.4.1620-1627.2006

Figure Lengend Snippet: Formation of plaques on confluent monolayers of HeLa and Caco-2 cells a

Article Snippet: The locations of 3× FLAG-tagged OspB recombinant protein as well as of IpaB, IpaC, and apyrase proteins are indicated. na, not added. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Relevant genotype or characteristic(s) Source or reference Strains M90T Wild-type S. flexneri serotype 5a 32 HND115 M90T Δ phoN2 ; susceptible This work HND201 M90T Δ ospB ; susceptible This work HND215 M90T Δ ospBphoN2 ; susceptible This work HND43 M90T Δ mxiA ; susceptible This work HND53 M90T Δ virB :: aphA-3 ; Km r This work HND549 M90T ospB -3×FLAG; susceptible This work HND5311 M90T Δ mxiA ospB -3×FLAG; susceptible This work SC560 M90T Δ icsA ::Ω; Sm r 10 M15[pREP4] E. coli K-12 strain carrying plasmid pREP4 Qiagen Plasmids pGEM-T Cloning vector, Ap r Promega pBluescript SK Cloning vector, Ap r Stratagene Inc., La Jolla, CA pBAD28 Arabinose-inducible P BAD expression vector, Ap r Cm r 13 pSUB11 Template plasmid carrying a 3×FLAG epitope and Km r cassette 42 pKD46 λ Red helper plasmid; oriR101 repA101 (Ts) P-araB-gam-bet-exo Ap r 7 pKD4 Template plasmid carrying a Km r gene with FLP recognition target sequence 7 pCP20 FLP helper plasmid; pSC101 replicon (Ts) bla cat Flp (λR p ) cI 857 Ap r Cm r 7 pREP4 lacI , Km r Qiagen pQE30 Cloning vector; Ap r Qiagen pHN301 pQE30 carrying His6- phoN2 ; Ap r This work pHN28 pBAD28 carrying phoN2 ; Ap r Cm r This work pHN111 pBAD28 carrying mxiA ; Ap r Cm r This work pFB1-4 pBluescript SK carrying a mutated phoN2 gene of EIEC strain HN280 presenting the R192P amino acid substitution 36 Open in a separate window a Ap r , ampicillin resistance; Cm r , cloramphenicol resistance; Km r , kanamycin resistance.

Techniques:

Journal:

Article Title: Apyrase, the Product of the Virulence Plasmid-Encoded phoN2 ( apy ) Gene of Shigella flexneri , Is Necessary for Proper Unipolar IcsA Localization and for Efficient Intercellular Spread †

doi: 10.1128/JB.188.4.1620-1627.2006

Figure Lengend Snippet: phoN2 mutant strain HND115 forms plaques of approximately wild-type size on Caco-2 cell monolayers when complemented with plasmid pFB1-4. pFB1-4 (Table ​(Table1)1) contains a randomly generated mutant of the apy gene, the orthologue of phoN2 in the EIEC strain HN280, encoding a recombinant apyrase presenting the R192P substitution which inactivates its dNTP-hydrolyzing activity. (A) Western blot analysis with anti-apyrase antibodies of whole-cell extracts of M90T, HND115 (phoN2), and HND115/pFB1-4 (pBluescript SKapyR192P). (B) Plaques formed by M90T, HND115 (phoN2), and HND115/pFB1-4 (pBluescript SKapyR192P). Dishes were photographed after 48 h of infection.

Article Snippet: The locations of 3× FLAG-tagged OspB recombinant protein as well as of IpaB, IpaC, and apyrase proteins are indicated. na, not added. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Relevant genotype or characteristic(s) Source or reference Strains M90T Wild-type S. flexneri serotype 5a 32 HND115 M90T Δ phoN2 ; susceptible This work HND201 M90T Δ ospB ; susceptible This work HND215 M90T Δ ospBphoN2 ; susceptible This work HND43 M90T Δ mxiA ; susceptible This work HND53 M90T Δ virB :: aphA-3 ; Km r This work HND549 M90T ospB -3×FLAG; susceptible This work HND5311 M90T Δ mxiA ospB -3×FLAG; susceptible This work SC560 M90T Δ icsA ::Ω; Sm r 10 M15[pREP4] E. coli K-12 strain carrying plasmid pREP4 Qiagen Plasmids pGEM-T Cloning vector, Ap r Promega pBluescript SK Cloning vector, Ap r Stratagene Inc., La Jolla, CA pBAD28 Arabinose-inducible P BAD expression vector, Ap r Cm r 13 pSUB11 Template plasmid carrying a 3×FLAG epitope and Km r cassette 42 pKD46 λ Red helper plasmid; oriR101 repA101 (Ts) P-araB-gam-bet-exo Ap r 7 pKD4 Template plasmid carrying a Km r gene with FLP recognition target sequence 7 pCP20 FLP helper plasmid; pSC101 replicon (Ts) bla cat Flp (λR p ) cI 857 Ap r Cm r 7 pREP4 lacI , Km r Qiagen pQE30 Cloning vector; Ap r Qiagen pHN301 pQE30 carrying His6- phoN2 ; Ap r This work pHN28 pBAD28 carrying phoN2 ; Ap r Cm r This work pHN111 pBAD28 carrying mxiA ; Ap r Cm r This work pFB1-4 pBluescript SK carrying a mutated phoN2 gene of EIEC strain HN280 presenting the R192P amino acid substitution 36 Open in a separate window a Ap r , ampicillin resistance; Cm r , cloramphenicol resistance; Km r , kanamycin resistance.

Techniques: Mutagenesis, Plasmid Preparation, Generated, Recombinant, Activity Assay, Western Blot, Infection

Journal:

Article Title: Differential Regulation of the PanA and PanB Proteasome-Activating Nucleotidase and 20S Proteasomal Proteins of the Haloarchaeon Haloferax volcanii †

doi: 10.1128/JB.186.22.7763-7772.2004

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: This exponential-phase culture was used as a 1% (vol/vol) inoculum into fresh medium for the analysis. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Phenotype, genotype, or oligonucleotides for PCR amplification Source E. coli strains DH5α F − recA1 endA1 hsdR17 (r k − m k + ) supE44 thi-1 gyrA relA1 Life Technologies BL21(DE3) F − ompT [ Ion ] hsd S B (r B m B ) (an E. coli B strain) with DE3, a λ prophage carrying the T7 RNA polymerase gene Novagen ER1647 F − fhuA2Δ ( lacZ ) r1 supE44 trp31 mcrA1272 ::Tn 10 (Tet r ) his-1 rpsL104 (Str r ) xyl-7 mtl-2 metB1 Δ ( mcrC-mrr ) 102 ::Tn 10 (Tet r ) recD1040 Novagen H. volcanii strains DS2 Isolate from the Dead Sea 23 DS70 DS2 cured of pHV2 36 WFD11 DS2 cured of pHV2 5 Plasmids pUC19 Ap r ; cloning vector New England BioLabs pCR-BluntII-TOPO Km r ; cloning vector InVitrogen pET24b Km r ; expression vector Novagen pJAM806 Ap r ; 0.36-kb PCR fragment of H. volcanii genomic DNA blunt-end ligated into HincII site of pUC19; carries pan -specific probe used in Southern blotting This study pJAM624 Ap r ; 2.7-kb Rsr II fragment of H. volcanii genomic DNA ligated into SmaI site of pUC19; carries panB ′ This study pJAM626 Ap r ; 6.2-kb SmaI fragment of H. volcanii genomic DNA ligated into HincII site of pUC19; carries panA This study pJAM631 Ap r ; 2.2-kb SacII genomic fragment from H. volcanii blunt-end ligated into HincII site of pUC19; carries panA This study pJAM638 Km r ; 1.2-kb fragment generated by PCR amplification from pJAM631 cloned into pCR-BluntII-TOPO; carries panA without a stop codon; 5′- CATATG ATGACCG ATACTGTGGAC-3′ and 5′- AGGCTT AGCAAACGCGCGGGAGAC-3′ (NdeI and HindIII sites in bold) pJAM639 Km r ; 1.1-kb fragment generated by PCR amplification from pJAM631 cloned into pCR-BluntII-TOPO; carries panA Δ 120 without a stop codon; 5′- CATATG CGC GACAAGCTCCTCGAC-3′ and 5′- AGGCTT AGCAAACGCGCGGGAGAC-3′ (NdeI and HindIII sites in bold) This study pJAM642 Km r ; 1.2-kb NdeI-to-HindIII fragment of pJAM638 ligated into NdeI and HindIII sites of pET24b; PanA-His expressed in E. coli This study pJAM643 Km r ; 1.1-kb NdeI-to-HindIII fragment of pJAM639 ligated into NdeI and HindIII sites of pET24b; PanA(Δ1-40)-His expressed in E. coli This study pJAM1006 Km r ; 1.24-kb fragment PCR amplified from H. volcanii genomic DNA ligated into NdeI and XhoI sites of pET24b; PanB-His expressed in E. coli; 5′- CATATG TCA CGCAGTCCATCTCTCC-3′ and 5′- CTCGAG GTACTGGTAGTCCGTGAAG-3′ (NdeI and XhoI sites indicated in bold) This study Open in a separate window Strains and plasmids used in this study

Techniques: Plasmid Preparation, Amplification, Cloning, Expressing, Southern Blot, Generated, Clone Assay

Journal: Microbiology Spectrum

Article Title: Phylogenomic, structural, and cell biological analyses reveal that Stenotrophomonas maltophilia replicates in acidified Rab7A-positive vacuoles of Acanthamoeba castellanii

doi: 10.1128/spectrum.02988-23

Figure Lengend Snippet: Strains and plasmids used and constructed in this study

Article Snippet: pUC18T-mini-Tn7T , Empty mini-Tn7 base vector (Ap R ) with transcriptional terminator and oriT; 3,515 bp. , AddGene #64957.

Techniques: Construct, Cloning, Expressing, Transfection, Plasmid Preparation, Control, Derivative Assay, Clone Assay, Bacteria, Chloramphenicol Acetyltransferase Assay, Labeling

Journal:

Article Title: Cloning and Characterization of the Bile Salt Hydrolase Genes ( bsh ) from Bifidobacterium bifidum Strains

doi: 10.1128/AEM.70.9.5603-5612.2004

Figure Lengend Snippet: Bacterial strains and plasmids used in this study

Article Snippet: When appropriate, ampicillin (200 μg/ml) and kanamycin (40 μg/ml) were added. table ft1 table-wrap mode="anchored" t5 TABLE 1. caption a7 Strain or plasmid Origin or relevant characteristics Source or reference Bacterial strains B. bifidum ATCC 11863 Wild type for cloning ATCC B. bifidum ATCC 35914 Human feces ATCC B. bifidum ATCC 15696 Infant intestine ATCC B. bifidum ATCC 29521 Type strain; infant feces ATCC B. bifidum KL 301 Dairy isolate This study B. bifidum KL 306 Dairy isolate This study B. adolescentis ATCC 15703 Type strain; adult intestine ATCC B. longum ATCC 15707 Type strain; adult intestine ATCC B. infantis ATCC 15697 Type strain; infant intestine ATCC B. breve ATCC 15707 Type strain; infant intestine ATCC E. coli DH5α F − φ80d lacZ ΔM15 Δ( lacZYA-argF ) U169 endA1 recA1 hsdR17 (r K − m K + ) deoR GIBCO-BRL E. coli BL21(DE3) F − ompT hsdS B (r B − m B − ) gal dcm lacY1 (DE3) Novagen Plasmids pBR322 Ap r ; cloning vector Invitrogen pUC19 Ap r ; cloning vector Invitrogen pDrive Ap r Kan r ; U-overhang PCR cloning vector QIAGEN pET36b(+) Kan r ; E. coli expression vector Novagen pBSH14 pBR322 with 3.5-kb B. bifidum ATCC 11863 chromosomal insert; BSH + This study pBSH27 pBR322 with 7.5-kb B. bifidum ATCC 11863 chromosomal insert; BSH + This study pBSH274 pUC19 with 4.0-kb Pst I insert from pBSH27; BSH + This study pDB150 pDrive with 1.5-kb PCR product; BSH + This study pUCB150 pUC19 with 1.5-kb Hind III & Kpn I insert from pDB150; BSH + This study pDB095 pDrive with 950-bp PCR product; BSH + This study pUCB095 pUC19 with 950-bp Hind III & Kpn I insert from pDB095; BSH − This study pBSH36b pET36b(+) with 950-bp Nde I & Hind III insert from pDB095; BSH + This study pBCS pDB095 with Cys-1-Ser mutation; BSH − This study pBCT pDB095 with Cys-1-Thr mutation; BSH − This study Open in a separate window Bacterial strains and plasmids used in this study Enzyme purification.

Techniques: Plasmid Preparation, Clone Assay, PCR Cloning, Expressing, Mutagenesis