φx174 Search Results


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  • 87
    New England Biolabs phix174 rf i dna
    Phix174 Rf I Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    φx174  (ATCC)
    99
    ATCC φx174
    A) Digital detection of phage particles after droplet PCR. Bacteriophages T4 and <t>ΦX174</t> virions are partitioned into droplets for TaqMan PCR detection. Scale bars are 100μm. B) Plaque assay results closely mimic digital viral particle quantitation, suggesting that phage genomes are accurately measured with this new method. Error bars represent the standard deviation of 3 technical replicates.
    φx174, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    ATCC bacteriophage φx174
    A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) <t>φX174</t> and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).
    Bacteriophage φx174, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    New England Biolabs phix174 virion dna
    A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) <t>φX174</t> and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).
    Phix174 Virion Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Promega supercoiled φx174 dsdna
    DNA strand exchange activity of RAD51 E258A versus WT with homologous ϕX174 DNA substrates and RPA protein (A) Reaction schematic. See Materials and Methods for details. (B) Timecourses of reactions containing a total of 7.50 μM RAD51 protein (WT and/or E258A) at the indicated concentrations. ssDNA (SS), <t>dsDNA</t> (LDS), nicked (NC), and <t>supercoiled</t> (SC) ϕX174 DNA markers (lanes 1–3, 22–24) and joint molecule (JM) products are indicated next to the gel. Left (lanes 4–9)-- Reaction with WT only; Center (lanes 10–15)-- Reaction with E258A only; Right (lanes 16–21)-- Reaction with 1:1 mixture of WT and E258A. All other experimental conditions were as described in Materials and Methods. (C) Quantitative analysis of joint molecule formation based on image scans were performed as described in Materials and Methods. Data are normalized relative to the total density of the Joint Molecules products formed by wild-type RAD51 at the 40 min time point. Results in panels (B) – (C) are typical of those obtained in three separate experiments performed under identical conditions.
    Supercoiled φx174 Dsdna, supplied by Promega, used in various techniques. Bioz Stars score: 89/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher phage φx174
    DNA strand exchange activity of RAD51 E258A versus WT with homologous ϕX174 DNA substrates and RPA protein (A) Reaction schematic. See Materials and Methods for details. (B) Timecourses of reactions containing a total of 7.50 μM RAD51 protein (WT and/or E258A) at the indicated concentrations. ssDNA (SS), <t>dsDNA</t> (LDS), nicked (NC), and <t>supercoiled</t> (SC) ϕX174 DNA markers (lanes 1–3, 22–24) and joint molecule (JM) products are indicated next to the gel. Left (lanes 4–9)-- Reaction with WT only; Center (lanes 10–15)-- Reaction with E258A only; Right (lanes 16–21)-- Reaction with 1:1 mixture of WT and E258A. All other experimental conditions were as described in Materials and Methods. (C) Quantitative analysis of joint molecule formation based on image scans were performed as described in Materials and Methods. Data are normalized relative to the total density of the Joint Molecules products formed by wild-type RAD51 at the 40 min time point. Results in panels (B) – (C) are typical of those obtained in three separate experiments performed under identical conditions.
    Phage φx174, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega hae iii digested φx174 dna molecular size markers
    DNA strand exchange activity of RAD51 E258A versus WT with homologous ϕX174 DNA substrates and RPA protein (A) Reaction schematic. See Materials and Methods for details. (B) Timecourses of reactions containing a total of 7.50 μM RAD51 protein (WT and/or E258A) at the indicated concentrations. ssDNA (SS), <t>dsDNA</t> (LDS), nicked (NC), and <t>supercoiled</t> (SC) ϕX174 DNA markers (lanes 1–3, 22–24) and joint molecule (JM) products are indicated next to the gel. Left (lanes 4–9)-- Reaction with WT only; Center (lanes 10–15)-- Reaction with E258A only; Right (lanes 16–21)-- Reaction with 1:1 mixture of WT and E258A. All other experimental conditions were as described in Materials and Methods. (C) Quantitative analysis of joint molecule formation based on image scans were performed as described in Materials and Methods. Data are normalized relative to the total density of the Joint Molecules products formed by wild-type RAD51 at the 40 min time point. Results in panels (B) – (C) are typical of those obtained in three separate experiments performed under identical conditions.
    Hae Iii Digested φx174 Dna Molecular Size Markers, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher supercoiled φx174 dna
    Comparative experiments of the oxidative cleavage of <t>ΦX174</t> plasmid <t>DNA</t> performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA
    Supercoiled φx174 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Promega φx174 dna hinfi dephosphorylated dna fragments
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna Hinfi Dephosphorylated Dna Fragments, supplied by Promega, used in various techniques. Bioz Stars score: 86/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher φx174 dna hinfi marker
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna Hinfi Marker, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc φx174 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher φx174 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega φx174 double stranded plasmid dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Double Stranded Plasmid Dna, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Promega φx174 hae iii
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Hae Iii, supplied by Promega, used in various techniques. Bioz Stars score: 88/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    TaKaRa φx174 hae iii
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Hae Iii, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher φx174 replicative form dna hae iii fragments
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Replicative Form Dna Hae Iii Fragments, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher φx174 rf1 dna
    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged <t>DNA;</t> lane 9 , end-labeled ϕX174 <t>HinfI</t> DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.
    φx174 Rf1 Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    φx174  (DSMZ)
    90
    DSMZ φx174
    Positions of mutations in <t>φX174</t> genome. The figure shows a 832-bp region of interest, including genes C , D , E , and J . Gene C is involved in DNA replication, gene D is an external scaffolding protein required for procapsid morphogenesis, gene E is responsible for lysis of the host, and gene J is required for DNA packaging ( Fane et al. 2006 ). Gene E is shown in three sections, corresponding to three domains of the protein. The transmembrane domain binds the E protein’s substrate, MraY ( Mendel et al. 2006 ; Zheng et al. 2009 ). Mutations are indicated with pins at the position, and the site and nucleotide change are indicated to the right of the pin head. The clone(s) carrying each mutation is indicated in parentheses. Note that one of the five background nucleotide differences between the Epos and D -promoter mutants (G833A) is included in this figure.
    φx174, supplied by DSMZ, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher 5 end labeled hin fi digested φx174 single stranded dna
    Positions of mutations in <t>φX174</t> genome. The figure shows a 832-bp region of interest, including genes C , D , E , and J . Gene C is involved in DNA replication, gene D is an external scaffolding protein required for procapsid morphogenesis, gene E is responsible for lysis of the host, and gene J is required for DNA packaging ( Fane et al. 2006 ). Gene E is shown in three sections, corresponding to three domains of the protein. The transmembrane domain binds the E protein’s substrate, MraY ( Mendel et al. 2006 ; Zheng et al. 2009 ). Mutations are indicated with pins at the position, and the site and nucleotide change are indicated to the right of the pin head. The clone(s) carrying each mutation is indicated in parentheses. Note that one of the five background nucleotide differences between the Epos and D -promoter mutants (G833A) is included in this figure.
    5 End Labeled Hin Fi Digested φx174 Single Stranded Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Promega assays bacteriophage φx174
    Virus spiking after filter preconditioning to 60% flow decay elevates LRV in a BSA concentration-dependent manner Spiked feeds were prepared to final mock MMV and <t>ΦX174</t> final concentrations of 0.5% and 2×10 8 pfu/ml respectively. ( A ) Non-spiked BSA at 1.0 g/l was processed to either 30 or 60% flow decay (V30 or V60), followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel (two-tailed, unpaired Student t test; P =0.0012). ( B ) Non-spiked BSA at 3.2 g/l was processed to either 30 or 60% flow decay (V30 or V60) followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel. In both ( A ) and ( B ), LRV 75 was determined by comparing total virus loaded on to the filters with total virus in the filtrates. Hold-up volume of the devices was factored into the calculation for total virus loaded. All conditions were run concurrently with five devices tested per condition.
    Assays Bacteriophage φx174, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    A) Digital detection of phage particles after droplet PCR. Bacteriophages T4 and ΦX174 virions are partitioned into droplets for TaqMan PCR detection. Scale bars are 100μm. B) Plaque assay results closely mimic digital viral particle quantitation, suggesting that phage genomes are accurately measured with this new method. Error bars represent the standard deviation of 3 technical replicates.

    Journal: Journal of virological methods

    Article Title: PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts

    doi: 10.1016/j.jviromet.2016.12.009

    Figure Lengend Snippet: A) Digital detection of phage particles after droplet PCR. Bacteriophages T4 and ΦX174 virions are partitioned into droplets for TaqMan PCR detection. Scale bars are 100μm. B) Plaque assay results closely mimic digital viral particle quantitation, suggesting that phage genomes are accurately measured with this new method. Error bars represent the standard deviation of 3 technical replicates.

    Article Snippet: T4 was propagated by infection of E. coli B (ATCC 11303) ( ) and ΦX174 by infection of E. coli C (ATCC 13706).

    Techniques: Polymerase Chain Reaction, Plaque Assay, Quantitation Assay, Standard Deviation

    A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) φX174 and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).

    Journal: Applied and Environmental Microbiology

    Article Title: Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters

    doi: 10.1128/AEM.02806-07

    Figure Lengend Snippet: A typical SPR reflectance angle minimum-time response used for the detection of bacteriophage (b. phage) φX174 and other somatic coliphages present in the wastewater samples. Arrows indicate the different steps from the cycle that were described in Materials and Methods: (i) incubation of the host strain E. coli WG5, (ii) PBS washing, and (iii) addition of the sample bacteriophage in one chamber (and negative control in the other chamber).

    Article Snippet: Bacteriophage φX174 (ATCC 13706-B1) was used as a reference bacteriophage for somatic coliphages.

    Techniques: SPR Assay, Incubation, Negative Control

    Variation of the reflectance angle minimum in response time detection with different concentrations of bacteriophages. (a) Detection of various concentrations of bacteriophage φX174 as measured by the SPR minimum angle change with time. Threshold time for 10 8 PFU/ml φX174 is marked on the plot for illustration. (b) Mean values of SPR minimum angle with time for detection of somatic coliphages in wastewater samples. Error bars show standard errors for triplicate repeats.

    Journal: Applied and Environmental Microbiology

    Article Title: Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters

    doi: 10.1128/AEM.02806-07

    Figure Lengend Snippet: Variation of the reflectance angle minimum in response time detection with different concentrations of bacteriophages. (a) Detection of various concentrations of bacteriophage φX174 as measured by the SPR minimum angle change with time. Threshold time for 10 8 PFU/ml φX174 is marked on the plot for illustration. (b) Mean values of SPR minimum angle with time for detection of somatic coliphages in wastewater samples. Error bars show standard errors for triplicate repeats.

    Article Snippet: Bacteriophage φX174 (ATCC 13706-B1) was used as a reference bacteriophage for somatic coliphages.

    Techniques: SPR Assay

    Inactivation kinetics of bacteriophages MS2 (A) and ϕX174 (B) and human viruses HAdV (C) and EV (D). The experiments were conducted in Swiss tap water at 22°C in 0.5-liter PET bottles that were either kept in the dark or exposed to SODIS.

    Journal: Applied and Environmental Microbiology

    Article Title: Solar Disinfection of Viruses in Polyethylene Terephthalate Bottles

    doi: 10.1128/AEM.02897-15

    Figure Lengend Snippet: Inactivation kinetics of bacteriophages MS2 (A) and ϕX174 (B) and human viruses HAdV (C) and EV (D). The experiments were conducted in Swiss tap water at 22°C in 0.5-liter PET bottles that were either kept in the dark or exposed to SODIS.

    Article Snippet: Phage MS2 (DSMZ 3767) and ϕX174 (ATCC 13706-B1) stocks were propagated and purified as described previously ( ).

    Techniques: Positron Emission Tomography

    DNA strand exchange activity of RAD51 E258A versus WT with homologous ϕX174 DNA substrates and RPA protein (A) Reaction schematic. See Materials and Methods for details. (B) Timecourses of reactions containing a total of 7.50 μM RAD51 protein (WT and/or E258A) at the indicated concentrations. ssDNA (SS), dsDNA (LDS), nicked (NC), and supercoiled (SC) ϕX174 DNA markers (lanes 1–3, 22–24) and joint molecule (JM) products are indicated next to the gel. Left (lanes 4–9)-- Reaction with WT only; Center (lanes 10–15)-- Reaction with E258A only; Right (lanes 16–21)-- Reaction with 1:1 mixture of WT and E258A. All other experimental conditions were as described in Materials and Methods. (C) Quantitative analysis of joint molecule formation based on image scans were performed as described in Materials and Methods. Data are normalized relative to the total density of the Joint Molecules products formed by wild-type RAD51 at the 40 min time point. Results in panels (B) – (C) are typical of those obtained in three separate experiments performed under identical conditions.

    Journal: DNA repair

    Article Title: Defects in Recombination Activity Caused by Somatic and Germline Mutations in the Multimerization/BRCA2 Binding Region of Human RAD51 Protein

    doi: 10.1016/j.dnarep.2017.10.008

    Figure Lengend Snippet: DNA strand exchange activity of RAD51 E258A versus WT with homologous ϕX174 DNA substrates and RPA protein (A) Reaction schematic. See Materials and Methods for details. (B) Timecourses of reactions containing a total of 7.50 μM RAD51 protein (WT and/or E258A) at the indicated concentrations. ssDNA (SS), dsDNA (LDS), nicked (NC), and supercoiled (SC) ϕX174 DNA markers (lanes 1–3, 22–24) and joint molecule (JM) products are indicated next to the gel. Left (lanes 4–9)-- Reaction with WT only; Center (lanes 10–15)-- Reaction with E258A only; Right (lanes 16–21)-- Reaction with 1:1 mixture of WT and E258A. All other experimental conditions were as described in Materials and Methods. (C) Quantitative analysis of joint molecule formation based on image scans were performed as described in Materials and Methods. Data are normalized relative to the total density of the Joint Molecules products formed by wild-type RAD51 at the 40 min time point. Results in panels (B) – (C) are typical of those obtained in three separate experiments performed under identical conditions.

    Article Snippet: Supercoiled φX174 dsDNA (5.4 kbp) was purchased from Promega and was linearized by digestion with PstI restriction endonuclease.

    Techniques: Activity Assay, Recombinase Polymerase Amplification

    Comparative experiments of the oxidative cleavage of ΦX174 plasmid DNA performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA

    Journal: Journal of Biological Inorganic Chemistry

    Article Title: DNA cleavage and binding selectivity of a heterodinuclear Pt-Cu(3-Clip-Phen) complex

    doi: 10.1007/s00775-008-0346-y

    Figure Lengend Snippet: Comparative experiments of the oxidative cleavage of ΦX174 plasmid DNA performed by 2 and 3 . Lane 1 control DNA. Lane 2 250 nM solution of 2 . Lane 3 50 nM 2 , in the presence of 5 mM mercaptopropionic acid (MPA). Lane 4 100 nM 2 , in the presence of 5 mM MPA. Lane 5 250 nM 2 , in the presence of 5 mM MPA. Lane 6 250 nM 3 . Lane 7 50 nM 3 , in the presence of 5 mM MPA. Lane 8 100 nM 3 , in the presence of 5 mM MPA. Lane 9 250 nM 3 , in the presence of 5 mM MPA

    Article Snippet: Five microliters of the complex solution was added to 10 μL of supercoiled ΦX174 DNA (Invitrogen, 7 nM, 40 μM base pairs) in 6 mM NaCl, 20 mM sodium phosphate buffer (pH 7.2), and incubated for 20 h at 37 °C.

    Techniques: Plasmid Preparation

    In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged DNA; lane 9 , end-labeled ϕX174 HinfI DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.

    Journal: The Journal of Biological Chemistry

    Article Title: Preferential Repair of Oxidized Base Damage in the Transcribed Genes of Mammalian Cells *

    doi: 10.1074/jbc.M110.198796

    Figure Lengend Snippet: In vitro reconstitution of TC-BER. For radioactive incorporation into pUC-TS-5-OHU (with [α- 32 P]dTMP ( lanes 1–7 ) or [α- 32 P]dAMP ( lane 8 )), 10 pmol of substrate was incubated with 0.5 pmol of NEIL2 ( lanes 1 and 3–8 ), 25 fmol of PNK, 0.25 pmol each of Pol β and Lig IIIα, and an RNAP II fraction containing TBP, TFIIB, and E/F/H (Protein One, except in lane 5 without the transcription factors) in the presence (+) or absence (−) of NTPs, as described under “Experimental Procedures.” Lane 1 , undamaged DNA; lane 9 , end-labeled ϕX174 HinfI DNA marker (Promega). Complete repair is indicated by the [ 32 P]dTMP incorporation. The repaired plasmid was linearized with EcoRI/HindIII and analyzed in a 6% TBE-urea gel; the gel was dried and the reaction products were analyzed and quantitated with a PhosphorImager. Bottom , histograms indicating the -fold increase in repair activity; activity without NTPs ( lane 3 ) was set to 1. Error bars , S.E.

    Article Snippet: The reactions were carried out at 30 °C for 90 min in a 50-μl reaction mixture and then stopped with 2% SDS in 0.2 m Tris-HCl (pH 7.5) and 10 μg/ml proteinase K. The nucleic acids were precipitated with ethanol, digested with EcoRI/HindIII, and once again ethanol-precipitated before final resuspension in formamide dye and denaturation at 90 °C for 3 min. Products were resolved alongside a φX174 HinfI DNA marker (Promega) on a 6% denaturing polyacrylamide gel in Tris borate-EDTA containing 8 m urea.

    Techniques: In Vitro, Incubation, Labeling, Marker, Plasmid Preparation, Activity Assay

    Positions of mutations in φX174 genome. The figure shows a 832-bp region of interest, including genes C , D , E , and J . Gene C is involved in DNA replication, gene D is an external scaffolding protein required for procapsid morphogenesis, gene E is responsible for lysis of the host, and gene J is required for DNA packaging ( Fane et al. 2006 ). Gene E is shown in three sections, corresponding to three domains of the protein. The transmembrane domain binds the E protein’s substrate, MraY ( Mendel et al. 2006 ; Zheng et al. 2009 ). Mutations are indicated with pins at the position, and the site and nucleotide change are indicated to the right of the pin head. The clone(s) carrying each mutation is indicated in parentheses. Note that one of the five background nucleotide differences between the Epos and D -promoter mutants (G833A) is included in this figure.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

    doi: 10.1534/g3.115.024075

    Figure Lengend Snippet: Positions of mutations in φX174 genome. The figure shows a 832-bp region of interest, including genes C , D , E , and J . Gene C is involved in DNA replication, gene D is an external scaffolding protein required for procapsid morphogenesis, gene E is responsible for lysis of the host, and gene J is required for DNA packaging ( Fane et al. 2006 ). Gene E is shown in three sections, corresponding to three domains of the protein. The transmembrane domain binds the E protein’s substrate, MraY ( Mendel et al. 2006 ; Zheng et al. 2009 ). Mutations are indicated with pins at the position, and the site and nucleotide change are indicated to the right of the pin head. The clone(s) carrying each mutation is indicated in parentheses. Note that one of the five background nucleotide differences between the Epos and D -promoter mutants (G833A) is included in this figure.

    Article Snippet: We studied the performance of φX174 on E. coli C [DSMZ 13127, kindly provided by Olivier Tenaillion, Institut National de la Santé et de la Recherche Médicale (INSERM), University Denis Diderot Paris 7], the phage’s natural host.

    Techniques: Scaffolding, Lysis, Mutagenesis

    Virus spiking after filter preconditioning to 60% flow decay elevates LRV in a BSA concentration-dependent manner Spiked feeds were prepared to final mock MMV and ΦX174 final concentrations of 0.5% and 2×10 8 pfu/ml respectively. ( A ) Non-spiked BSA at 1.0 g/l was processed to either 30 or 60% flow decay (V30 or V60), followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel (two-tailed, unpaired Student t test; P =0.0012). ( B ) Non-spiked BSA at 3.2 g/l was processed to either 30 or 60% flow decay (V30 or V60) followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel. In both ( A ) and ( B ), LRV 75 was determined by comparing total virus loaded on to the filters with total virus in the filtrates. Hold-up volume of the devices was factored into the calculation for total virus loaded. All conditions were run concurrently with five devices tested per condition.

    Journal: Biotechnology and Applied Biochemistry

    Article Title: Filter preconditioning enables representative scaled-down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities

    doi: 10.1042/BA20080133

    Figure Lengend Snippet: Virus spiking after filter preconditioning to 60% flow decay elevates LRV in a BSA concentration-dependent manner Spiked feeds were prepared to final mock MMV and ΦX174 final concentrations of 0.5% and 2×10 8 pfu/ml respectively. ( A ) Non-spiked BSA at 1.0 g/l was processed to either 30 or 60% flow decay (V30 or V60), followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel (two-tailed, unpaired Student t test; P =0.0012). ( B ) Non-spiked BSA at 3.2 g/l was processed to either 30 or 60% flow decay (V30 or V60) followed by spiked feed to a 75% flow decay endpoint. Conventional spiking was also run in parallel. In both ( A ) and ( B ), LRV 75 was determined by comparing total virus loaded on to the filters with total virus in the filtrates. Hold-up volume of the devices was factored into the calculation for total virus loaded. All conditions were run concurrently with five devices tested per condition.

    Article Snippet: Viruses and assays Bacteriophage ΦX174 was purchased from Promega (Madison, WI, U.S.A.) and assayed as previously described [ ].

    Techniques: Flow Cytometry, Concentration Assay, Two Tailed Test

    Virus spike impurities accelerate membrane fouling Filtration hydraulic performance was compared for feeds with and without spike impurities. Non-spiked 1.0 g/l BSA was also processed. All filtrations were run under a constant pressure of 207 kPa (30 lbf/in 2 ). Flux was plotted against volumetric throughput. Five devices were tested simultaneously per condition and they demonstrated similar trends; representative results are shown for each condition. ( A ) 1.0 g/l BSA was spiked with either purified or crude MMV stocks to a final concentration of 2.5×10 6 TCID 50 /ml and filtered. ( B ) 1.0 g/l BSA was spiked to a final concentration of 2.0×10 8 pfu (plaque-forming units)/ml with either ΦX174 or ΦX174 plus 0.5% mock MMV stock, and filtered.

    Journal: Biotechnology and Applied Biochemistry

    Article Title: Filter preconditioning enables representative scaled-down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities

    doi: 10.1042/BA20080133

    Figure Lengend Snippet: Virus spike impurities accelerate membrane fouling Filtration hydraulic performance was compared for feeds with and without spike impurities. Non-spiked 1.0 g/l BSA was also processed. All filtrations were run under a constant pressure of 207 kPa (30 lbf/in 2 ). Flux was plotted against volumetric throughput. Five devices were tested simultaneously per condition and they demonstrated similar trends; representative results are shown for each condition. ( A ) 1.0 g/l BSA was spiked with either purified or crude MMV stocks to a final concentration of 2.5×10 6 TCID 50 /ml and filtered. ( B ) 1.0 g/l BSA was spiked to a final concentration of 2.0×10 8 pfu (plaque-forming units)/ml with either ΦX174 or ΦX174 plus 0.5% mock MMV stock, and filtered.

    Article Snippet: Viruses and assays Bacteriophage ΦX174 was purchased from Promega (Madison, WI, U.S.A.) and assayed as previously described [ ].

    Techniques: Filtration, Purification, Concentration Assay

    Virus stock impurities decrease volumetric throughput and artificially elevate virus retention in a concentration-dependent manner ΦX174 was added to 1.0 g/L BSA to a final concentration of 5.0×10 8 pfu/ml. Three feed solutions were prepared from this stock solution containing no mock MMV and final concentrations of 0.5 and 1% mock MMV. The feeds were filtered to 75% flow decay. Final pooled samples were assayed for infectivity using a standard plaque assay. LRV 75 was calculated based on the concentration of virus in the filtrates relative to the feed concentrations. Five devices were tested per condition. All conditions were tested concurrently (two-tailed, unpaired Student t test; P =0.0009).

    Journal: Biotechnology and Applied Biochemistry

    Article Title: Filter preconditioning enables representative scaled-down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities

    doi: 10.1042/BA20080133

    Figure Lengend Snippet: Virus stock impurities decrease volumetric throughput and artificially elevate virus retention in a concentration-dependent manner ΦX174 was added to 1.0 g/L BSA to a final concentration of 5.0×10 8 pfu/ml. Three feed solutions were prepared from this stock solution containing no mock MMV and final concentrations of 0.5 and 1% mock MMV. The feeds were filtered to 75% flow decay. Final pooled samples were assayed for infectivity using a standard plaque assay. LRV 75 was calculated based on the concentration of virus in the filtrates relative to the feed concentrations. Five devices were tested per condition. All conditions were tested concurrently (two-tailed, unpaired Student t test; P =0.0009).

    Article Snippet: Viruses and assays Bacteriophage ΦX174 was purchased from Promega (Madison, WI, U.S.A.) and assayed as previously described [ ].

    Techniques: Concentration Assay, Flow Cytometry, Infection, Plaque Assay, Two Tailed Test

    Filter preconditioning to 50% flow decay represents a safety limit to the complementary approach to virus filter validation BSA (1.0 g/l) was prepared for use as a model protein. An aliquot of 1.0 g/l BSA was spiked with a simulated virus stock to give mock MMV and ΦX174 final concentrations of 0.5% and 2×10 8 pfu/ml respectively. The remaining non-spiked BSA was processed to 50 or 60% flow decay. Spiked feed was introduced upon reaching these flow decay points and processed out to 75% flow decay. Spiked controls (conventional method) were run in parallel with the preconditioned challenges. LRV 75 was calculated based on the concentration of virus in the filtrates from only the spiked phase of the experiments relative to the feed concentrations. Hold-up volume of the devices was factored into the calculation for total virus loaded. All conditions were run concurrently with five devices tested per condition (two-tailed, unpaired Student t test; P =0.0032).

    Journal: Biotechnology and Applied Biochemistry

    Article Title: Filter preconditioning enables representative scaled-down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities

    doi: 10.1042/BA20080133

    Figure Lengend Snippet: Filter preconditioning to 50% flow decay represents a safety limit to the complementary approach to virus filter validation BSA (1.0 g/l) was prepared for use as a model protein. An aliquot of 1.0 g/l BSA was spiked with a simulated virus stock to give mock MMV and ΦX174 final concentrations of 0.5% and 2×10 8 pfu/ml respectively. The remaining non-spiked BSA was processed to 50 or 60% flow decay. Spiked feed was introduced upon reaching these flow decay points and processed out to 75% flow decay. Spiked controls (conventional method) were run in parallel with the preconditioned challenges. LRV 75 was calculated based on the concentration of virus in the filtrates from only the spiked phase of the experiments relative to the feed concentrations. Hold-up volume of the devices was factored into the calculation for total virus loaded. All conditions were run concurrently with five devices tested per condition (two-tailed, unpaired Student t test; P =0.0032).

    Article Snippet: Viruses and assays Bacteriophage ΦX174 was purchased from Promega (Madison, WI, U.S.A.) and assayed as previously described [ ].

    Techniques: Flow Cytometry, Concentration Assay, Two Tailed Test

    Virus retention is dependent on filter flow decay state rather than volumetric throughput Bacteriophage ΦX174 was added to three concentrations of a therapeutic protein and filtered. Instantaneous/grab filtrate samples were collected as the filtration progressed and samples were assayed using a standard plaque assay. Bacteriophage retention (LRV) was calculated by comparing filtrate titres with feed titres. LRV was plotted against ( A ) volumetric throughput (l/m 2 ) and ( B ) flow decay (%) relative to initial buffer flow rate.

    Journal: Biotechnology and Applied Biochemistry

    Article Title: Filter preconditioning enables representative scaled-down modelling of filter capacity and viral clearance by mitigating the impact of virus spike impurities

    doi: 10.1042/BA20080133

    Figure Lengend Snippet: Virus retention is dependent on filter flow decay state rather than volumetric throughput Bacteriophage ΦX174 was added to three concentrations of a therapeutic protein and filtered. Instantaneous/grab filtrate samples were collected as the filtration progressed and samples were assayed using a standard plaque assay. Bacteriophage retention (LRV) was calculated by comparing filtrate titres with feed titres. LRV was plotted against ( A ) volumetric throughput (l/m 2 ) and ( B ) flow decay (%) relative to initial buffer flow rate.

    Article Snippet: Viruses and assays Bacteriophage ΦX174 was purchased from Promega (Madison, WI, U.S.A.) and assayed as previously described [ ].

    Techniques: Flow Cytometry, Filtration, Plaque Assay