ph d 12 peptide library aliquot  (New England Biolabs)


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    Ph D 12 Phage Display Peptide Library
    Description:
    Ph D 12 Phage Display Peptide Library 50 panning exps
    Catalog Number:
    E8111L
    Price:
    2260
    Category:
    Phage Display Systems
    Size:
    50 exps
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    New England Biolabs ph d 12 peptide library aliquot
    Ph D 12 Phage Display Peptide Library
    Ph D 12 Phage Display Peptide Library 50 panning exps
    https://www.bioz.com/result/ph d 12 peptide library aliquot/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ph d 12 peptide library aliquot - by Bioz Stars, 2021-09
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    Images

    1) Product Images from "Identification of a peptide for folate receptor alpha by phage display and its tumor targeting activity in ovary cancer xenograft"

    Article Title: Identification of a peptide for folate receptor alpha by phage display and its tumor targeting activity in ovary cancer xenograft

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-26683-z

    Screening and identification of FRα binding peptides. A Ph.D.-12 phage library was used to screen FRα binding phages with four rounds of biopanning. ( A ) The enrichment of FRα binding phages were evaluated by phage recovery yields of each round selection. ( B ) Polyclonal phage ELISA using elutes after each round selection. ( C ) 94 phage clones were randomLy picked from the third round selection, and their binding affinities for FRα were analyzed individually by phage ELISA.
    Figure Legend Snippet: Screening and identification of FRα binding peptides. A Ph.D.-12 phage library was used to screen FRα binding phages with four rounds of biopanning. ( A ) The enrichment of FRα binding phages were evaluated by phage recovery yields of each round selection. ( B ) Polyclonal phage ELISA using elutes after each round selection. ( C ) 94 phage clones were randomLy picked from the third round selection, and their binding affinities for FRα were analyzed individually by phage ELISA.

    Techniques Used: Binding Assay, Selection, Enzyme-linked Immunosorbent Assay, Clone Assay

    2) Product Images from "Inter-molecular epitope spreading does not lead to extension of autoimmunity beyond target tissue in autoimmune glomerulonephritis"

    Article Title: Inter-molecular epitope spreading does not lead to extension of autoimmunity beyond target tissue in autoimmune glomerulonephritis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0202988

    Identification of novel epitopes in GBM proteins recognized by eluted anti-GBM autoantibodies using random phage display peptide library. ( A ) Western blot screening of phage clones for their surface protein p III that positively reacted to GBM autoantibodies. Phage clones were from repeated panning by anti-GBM autoantibodies. ( B ) Confirmation of a representative clone that displayed positive reactivity to anti-GBM autoantibodies but not rat IgG by Western blot. Only one positive and one negative clone are shown. Note that the positive clone reacted to the Ab but not rat IgG. ( C ) Phylogeny tree for DNA sequences of 36 bp inserts from clones in which their pIII reacted to anti-GBM autoantibodies. Four clusters, indicated as A, B, C and D, are shown. ( D ) Comparison of a.a. sequences of GBM proteins with those deduced from A, B, C and D. Highlighted (yellow) letters indicate the identical residues or motif. Underlined letters are the identified a.a. sequences of GBM proteins (shown at the left) with their positions noted as superscript numbers. Flank a.a. residues were added for synthesis of 15-mer peptides as shown at the right.
    Figure Legend Snippet: Identification of novel epitopes in GBM proteins recognized by eluted anti-GBM autoantibodies using random phage display peptide library. ( A ) Western blot screening of phage clones for their surface protein p III that positively reacted to GBM autoantibodies. Phage clones were from repeated panning by anti-GBM autoantibodies. ( B ) Confirmation of a representative clone that displayed positive reactivity to anti-GBM autoantibodies but not rat IgG by Western blot. Only one positive and one negative clone are shown. Note that the positive clone reacted to the Ab but not rat IgG. ( C ) Phylogeny tree for DNA sequences of 36 bp inserts from clones in which their pIII reacted to anti-GBM autoantibodies. Four clusters, indicated as A, B, C and D, are shown. ( D ) Comparison of a.a. sequences of GBM proteins with those deduced from A, B, C and D. Highlighted (yellow) letters indicate the identical residues or motif. Underlined letters are the identified a.a. sequences of GBM proteins (shown at the left) with their positions noted as superscript numbers. Flank a.a. residues were added for synthesis of 15-mer peptides as shown at the right.

    Techniques Used: Western Blot, Clone Assay

    3) Product Images from "Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs"

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    Journal: Viruses

    doi: 10.3390/v12121360

    Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.
    Figure Legend Snippet: Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.

    Techniques Used: Sequencing

    Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.
    Figure Legend Snippet: Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .
    Figure Legend Snippet: Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.
    Figure Legend Snippet: Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.

    Techniques Used:

    Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .
    Figure Legend Snippet: Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    4) Product Images from "Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization"

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-02891-x

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.
    Figure Legend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Techniques Used: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay

    5) Product Images from "Identification of Human Embryonic Progenitor Cell Targeting Peptides Using Phage Display"

    Article Title: Identification of Human Embryonic Progenitor Cell Targeting Peptides Using Phage Display

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0058200

    Selection of a peptide phage display library against W10 embryonic progenitor cells. (A) Peptide phages that bind to W10 embryonic progenitor cell line were enriched by 3 rounds of biopanning. PhD-12 phage display peptide library (2×10 11 pfu, for round 1) or amplified recovered phage (2×10 10 pfu, for rounds 2 and 3) were first adsorbed against human adult dermal fibroblasts cells and then incubated with adherent W10 cells. The phages were recovered from the cell lysate and sample phage clones were sequenced. The enriched library was amplified for further rounds of selection. (B) The percentage of input phages recovered increased with each round of selection. The percentage of input phages recovered was determined by titration of plaque forming units (pfu) in the cell lysate relative to the input pfu used for each panning round. (C) Frequency and multiple sequence alignment of peptides identified as candidate peptide phage in rounds 2 and 3 of panning generated by CLUSTAL W (2.10). (D) Phylogram based on (C) denoting peptide similarities.
    Figure Legend Snippet: Selection of a peptide phage display library against W10 embryonic progenitor cells. (A) Peptide phages that bind to W10 embryonic progenitor cell line were enriched by 3 rounds of biopanning. PhD-12 phage display peptide library (2×10 11 pfu, for round 1) or amplified recovered phage (2×10 10 pfu, for rounds 2 and 3) were first adsorbed against human adult dermal fibroblasts cells and then incubated with adherent W10 cells. The phages were recovered from the cell lysate and sample phage clones were sequenced. The enriched library was amplified for further rounds of selection. (B) The percentage of input phages recovered increased with each round of selection. The percentage of input phages recovered was determined by titration of plaque forming units (pfu) in the cell lysate relative to the input pfu used for each panning round. (C) Frequency and multiple sequence alignment of peptides identified as candidate peptide phage in rounds 2 and 3 of panning generated by CLUSTAL W (2.10). (D) Phylogram based on (C) denoting peptide similarities.

    Techniques Used: Selection, Amplification, Incubation, Clone Assay, Titration, Sequencing, Generated

    Phage binding competition with free peptide. Competition of the peptide phage with free peptide was measured using (A) Immunofluorescent detection of bound peptide phages. Chemically synthesized peptides were added to compete with binding of peptide phages to W10 progenitor cells. Cells were pre-incubated with different peptides at 100 µM or without peptide for 30 min at 4°C, followed by peptide phages (2×10 10 pfu) for an additional 1 h at 4°C. After washing, the bound peptide phages were detected by immunofluorescence. Peptide sequences are: W10-R2-11-biotin: GWVIDYDYYPMRGGGK(biotin); FITC-W10-R2-11: FITC-GWVIDYDYYPMRGGG and FITC-unrelated: FITC-NHVHRMHATPAY (B) Percentage of input phage recovered from cell lysate. Cells were pre-incubated with peptides at 5 µM or 5 nM, or without peptide for 30 min at 4°C, followed by peptide phages (2×10 10 pfu) for an additional 1h at 4°C. After washing, the recovered phage was quantified by titration. The competition is shown as percentage of no-peptide control. Values are from triplicate experiments shown as mean ± standard deviation. Competition by the corresponding free peptide was statistically significant at 5 nM and 5 µM with the exception of W10-R2-21 (only significant at 5 µM). Competition by scrambled or unrelated peptide was not statistically significant. (ANOVA with Dunnett’s multiple comparison tests; p values: *:
    Figure Legend Snippet: Phage binding competition with free peptide. Competition of the peptide phage with free peptide was measured using (A) Immunofluorescent detection of bound peptide phages. Chemically synthesized peptides were added to compete with binding of peptide phages to W10 progenitor cells. Cells were pre-incubated with different peptides at 100 µM or without peptide for 30 min at 4°C, followed by peptide phages (2×10 10 pfu) for an additional 1 h at 4°C. After washing, the bound peptide phages were detected by immunofluorescence. Peptide sequences are: W10-R2-11-biotin: GWVIDYDYYPMRGGGK(biotin); FITC-W10-R2-11: FITC-GWVIDYDYYPMRGGG and FITC-unrelated: FITC-NHVHRMHATPAY (B) Percentage of input phage recovered from cell lysate. Cells were pre-incubated with peptides at 5 µM or 5 nM, or without peptide for 30 min at 4°C, followed by peptide phages (2×10 10 pfu) for an additional 1h at 4°C. After washing, the recovered phage was quantified by titration. The competition is shown as percentage of no-peptide control. Values are from triplicate experiments shown as mean ± standard deviation. Competition by the corresponding free peptide was statistically significant at 5 nM and 5 µM with the exception of W10-R2-21 (only significant at 5 µM). Competition by scrambled or unrelated peptide was not statistically significant. (ANOVA with Dunnett’s multiple comparison tests; p values: *:

    Techniques Used: Binding Assay, Synthesized, Incubation, Immunofluorescence, Titration, Standard Deviation

    Binding of peptide display phages to W10 embryonic progenitor cell line. (A) Immunofluorescent detection of bound phages. Cells were incubated with 2×10 10 phage particles for 2 h at 37°C; unbound phages were removed by washing and cells were fixed and permeabilized. Bound phages were detected by immunocytochemistry using rabbit anti-phage antibody and Alexa568-conjugated goat anti-rabbit antibody. Cell nuclei were stained using DAPI. (B) Quantitation of peptide phage cell binding. 2×10 10 pfu of each candidate or controls (RGD, Gly12 and empty phage M13KE) phages were assessed for binding on 1×10 5 W10 progenitor cells for 2 h at 37°C. Cell associated phages were recovered from cell lysates and quantified by titration. Protein in cell lysates was measured by microBCA assay. The relative binding factor (BF) is calculated as peptide phage recovery (percentage of input) relative to M13KE control phage recovery (percentage of input). Values are from triplicate experiments and shown as mean ± standard deviation. BFs for the 4 W10 peptide phage were statistical significant from the control M13KE phage (ANOVA with Dunnett’s multiple comparison tests; p values: *:
    Figure Legend Snippet: Binding of peptide display phages to W10 embryonic progenitor cell line. (A) Immunofluorescent detection of bound phages. Cells were incubated with 2×10 10 phage particles for 2 h at 37°C; unbound phages were removed by washing and cells were fixed and permeabilized. Bound phages were detected by immunocytochemistry using rabbit anti-phage antibody and Alexa568-conjugated goat anti-rabbit antibody. Cell nuclei were stained using DAPI. (B) Quantitation of peptide phage cell binding. 2×10 10 pfu of each candidate or controls (RGD, Gly12 and empty phage M13KE) phages were assessed for binding on 1×10 5 W10 progenitor cells for 2 h at 37°C. Cell associated phages were recovered from cell lysates and quantified by titration. Protein in cell lysates was measured by microBCA assay. The relative binding factor (BF) is calculated as peptide phage recovery (percentage of input) relative to M13KE control phage recovery (percentage of input). Values are from triplicate experiments and shown as mean ± standard deviation. BFs for the 4 W10 peptide phage were statistical significant from the control M13KE phage (ANOVA with Dunnett’s multiple comparison tests; p values: *:

    Techniques Used: Binding Assay, Incubation, Immunocytochemistry, Staining, Quantitation Assay, Titration, Standard Deviation

    Labeling of embryonic progenitor cell line using peptide targeted Qdot605. (A) Cell targeting by fluorescent Qdots. Qdot605-ITK-SA were complexed with an excess of chemically synthesized C-terminal biotinylated peptide; unbound peptide was removed by dialysis. W10 progenitor cells were incubated for 16 h at 37°C with 5 nM of Qdot complexes, washed and imaged using a fluorescence microscope. (B) Competition with free peptide or peptide-targeted Qdots. Cells were pre-incubated with 5nM peptide, peptide targeted Qdots, or untargeted Qdots, for 30 min at 4°C, followed by addition of peptide phage (2×10 10 pfu) for an additional 1 h at 4°C. After washing, the recovered phage was quantified by titration. The competition is shown as percentage of no-peptide control. Values are from triplicate experiments and shown as mean ± standard deviation. Competition by corresponding free peptide or peptide-Qdot complex at 5 nM was statistically significant. Competition by uncoupled Qdots was not statistically significant (ANOVA with Dunnett’s multiple comparison tests; p values: *:
    Figure Legend Snippet: Labeling of embryonic progenitor cell line using peptide targeted Qdot605. (A) Cell targeting by fluorescent Qdots. Qdot605-ITK-SA were complexed with an excess of chemically synthesized C-terminal biotinylated peptide; unbound peptide was removed by dialysis. W10 progenitor cells were incubated for 16 h at 37°C with 5 nM of Qdot complexes, washed and imaged using a fluorescence microscope. (B) Competition with free peptide or peptide-targeted Qdots. Cells were pre-incubated with 5nM peptide, peptide targeted Qdots, or untargeted Qdots, for 30 min at 4°C, followed by addition of peptide phage (2×10 10 pfu) for an additional 1 h at 4°C. After washing, the recovered phage was quantified by titration. The competition is shown as percentage of no-peptide control. Values are from triplicate experiments and shown as mean ± standard deviation. Competition by corresponding free peptide or peptide-Qdot complex at 5 nM was statistically significant. Competition by uncoupled Qdots was not statistically significant (ANOVA with Dunnett’s multiple comparison tests; p values: *:

    Techniques Used: Labeling, Synthesized, Incubation, Fluorescence, Microscopy, Titration, Standard Deviation

    6) Product Images from "Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization"

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-02891-x

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.
    Figure Legend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Techniques Used: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay

    7) Product Images from "Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization"

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-02891-x

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.
    Figure Legend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Techniques Used: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay

    8) Product Images from "Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs"

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    Journal: Viruses

    doi: 10.3390/v12121360

    Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of  > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.
    Figure Legend Snippet: Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.

    Techniques Used: Sequencing

    Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.
    Figure Legend Snippet: Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3).  Figure A2 , which shows heatmaps of all fractions can be found in  Appendix A .
    Figure Legend Snippet: Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.
    Figure Legend Snippet: Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.

    Techniques Used:

    Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in  Section 3.6 .
    Figure Legend Snippet: Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    9) Product Images from "Induction of aquaporin 4-reactive antibodies in Lewis rats immunized with aquaporin 4 mimotopes"

    Article Title: Induction of aquaporin 4-reactive antibodies in Lewis rats immunized with aquaporin 4 mimotopes

    Journal: Acta Neuropathologica Communications

    doi: 10.1186/s40478-020-00920-x

    Characterization of NMO-IgGs used for mimotope search. a - d Immunofluorescence staining of Lewis rat astrocytes and analysis by confocal microscopy. The NMO-IgG preparation IV containing pathogenic AQP4-reactive antibodies recognizing conformational epitopes on the surface of astrocytes ( a , red), a commercial AQP4-reactive antibody recognizing intracellular AQP4 epitopes ( b , green) and an antibody directed against GFAP ( c , blue) were used for stainings. Stainings against surface and intracellular AQP4 epitopes were merged to prove that IV contains AQP4-reactive antibodies reacting with rat AQP4 ( d , white). e - f Formation of astrocyte-destructive lesions in experimental NMO. Shown here are spinal cords of Lewis rats injected with myelin basic protein-specific T cells and the NMO-IgG preparations IV ( e ), III ( f ) and I ( g ). Sections were stained with antibodies against AQP4 to show astrocytes (brown) and counterstained with hematoxylin to show nuclei (blue). h For each NMO-IgG preparation used, the phage display peptide library Ph.D.-12 was subjected to three rounds of negative selection on human control-IgG (Subcuvia) to deplete phages binding to “common antibodies”, and of positive selection on NMO-IgG to enrich for phages binding to the AQP4-reactive antibodies contained within the NMO-IgG preparation. At the end of these selections, bound phages were released, amplified, and sequenced for the identification of the mimotopes. i Example of sequencing results for mimotope IV-04. The DNA sequence represents the genomic (+) ssDNA in 5´➔ 3´ direction. Underneath you see the corresponding amino acid sequence (capital letters). Mimotope flanking regions are shown in gray, restriction enzyme recognitions sites in yellow and red, and the mimotope sequence in magenta
    Figure Legend Snippet: Characterization of NMO-IgGs used for mimotope search. a - d Immunofluorescence staining of Lewis rat astrocytes and analysis by confocal microscopy. The NMO-IgG preparation IV containing pathogenic AQP4-reactive antibodies recognizing conformational epitopes on the surface of astrocytes ( a , red), a commercial AQP4-reactive antibody recognizing intracellular AQP4 epitopes ( b , green) and an antibody directed against GFAP ( c , blue) were used for stainings. Stainings against surface and intracellular AQP4 epitopes were merged to prove that IV contains AQP4-reactive antibodies reacting with rat AQP4 ( d , white). e - f Formation of astrocyte-destructive lesions in experimental NMO. Shown here are spinal cords of Lewis rats injected with myelin basic protein-specific T cells and the NMO-IgG preparations IV ( e ), III ( f ) and I ( g ). Sections were stained with antibodies against AQP4 to show astrocytes (brown) and counterstained with hematoxylin to show nuclei (blue). h For each NMO-IgG preparation used, the phage display peptide library Ph.D.-12 was subjected to three rounds of negative selection on human control-IgG (Subcuvia) to deplete phages binding to “common antibodies”, and of positive selection on NMO-IgG to enrich for phages binding to the AQP4-reactive antibodies contained within the NMO-IgG preparation. At the end of these selections, bound phages were released, amplified, and sequenced for the identification of the mimotopes. i Example of sequencing results for mimotope IV-04. The DNA sequence represents the genomic (+) ssDNA in 5´➔ 3´ direction. Underneath you see the corresponding amino acid sequence (capital letters). Mimotope flanking regions are shown in gray, restriction enzyme recognitions sites in yellow and red, and the mimotope sequence in magenta

    Techniques Used: Immunofluorescence, Staining, Confocal Microscopy, Injection, Selection, Binding Assay, Amplification, Sequencing

    10) Product Images from "Membrane Protein Complex ExbB4-ExbD1-TonB1 from Escherichia coli Demonstrates Conformational Plasticity"

    Article Title: Membrane Protein Complex ExbB4-ExbD1-TonB1 from Escherichia coli Demonstrates Conformational Plasticity

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.00069-15

    (A and B) Alignment of ExbD 43–141 and TonB 33–239 affinity-selected Ph.D.-C7C and Ph.D.-12 peptides to the ExbD sequence. (A) The top 10 scoring ExbD 43–141 affinity-selected peptides aligned to residues 46 to 73 of the periplasmic domain of ExbD. See also Table S1 in the supplemental material for peptide match scores and window sizes. (B) The top nine scoring TonB 33–239 affinity-selected peptides aligned to residues 46 to 62 of the periplasmic domain of ExbD. See also Table S2 in the supplemental material for peptide match scores and window sizes. (C and D) Alignment of ExbD 43–141 affinity-selected Ph.D.-C7C and Ph.D.-12 peptides to TonB sequence. (C) The top six scoring peptides aligned to residues 38 to 55 of the periplasmic domain of TonB. (D) The top nine scoring peptides aligned to residues 125 to 144 of the central region of periplasmic TonB. See also Table S3 in the supplemental material for peptide match scores and window sizes. Only top-scoring peptides are shown for clarity; see the corresponding tables in the supplemental material for all peptides.
    Figure Legend Snippet: (A and B) Alignment of ExbD 43–141 and TonB 33–239 affinity-selected Ph.D.-C7C and Ph.D.-12 peptides to the ExbD sequence. (A) The top 10 scoring ExbD 43–141 affinity-selected peptides aligned to residues 46 to 73 of the periplasmic domain of ExbD. See also Table S1 in the supplemental material for peptide match scores and window sizes. (B) The top nine scoring TonB 33–239 affinity-selected peptides aligned to residues 46 to 62 of the periplasmic domain of ExbD. See also Table S2 in the supplemental material for peptide match scores and window sizes. (C and D) Alignment of ExbD 43–141 affinity-selected Ph.D.-C7C and Ph.D.-12 peptides to TonB sequence. (C) The top six scoring peptides aligned to residues 38 to 55 of the periplasmic domain of TonB. (D) The top nine scoring peptides aligned to residues 125 to 144 of the central region of periplasmic TonB. See also Table S3 in the supplemental material for peptide match scores and window sizes. Only top-scoring peptides are shown for clarity; see the corresponding tables in the supplemental material for all peptides.

    Techniques Used: Sequencing

    11) Product Images from "Generation of a novel therapeutic peptide that depletes MDSC in tumor-bearing mice"

    Article Title: Generation of a novel therapeutic peptide that depletes MDSC in tumor-bearing mice

    Journal: Nature medicine

    doi: 10.1038/nm.3560

    Identification and characterization of MDSC-binding peptides ( a ) Identification of Gr-1 + CD11b + MDSC in spleens of C57BL/6 mice ( n = 5) challenged subcutaneously with EL4 mouse lymphoma cells for 3 weeks. Double positive cells contain 2 distinct populations including Gr-1 high CD11b + granulocytic (P7) and Gr-1 int CD11b + monocytic (P10) MDSC subsets. ( b–c ) Biopanning with Ph.D.-12 peptide phage display library on Gr-1 and CD11b labeled splenocytes showed enriched phage eluted from sorted MDSC subsets. Biopanning enrichment was expressed in either “Number of plaques / 10 6 cells” or phage “Output / Input ratio” (× 10 –8 ). ( d ) Binding of synthetic FITC-conjugated G3 and H6 peptides on Gr-1 + CD11b + gated MDSC from EL4-bearing C57BL/6 mice ( n = 4), compared with Gr-1 − CD11b − gated non-MDSC splenocytes. A non-specific peptide (irrel peptide) was used as a negative control to exclude non-specific binding. The data are representative of 3 identical experiments.
    Figure Legend Snippet: Identification and characterization of MDSC-binding peptides ( a ) Identification of Gr-1 + CD11b + MDSC in spleens of C57BL/6 mice ( n = 5) challenged subcutaneously with EL4 mouse lymphoma cells for 3 weeks. Double positive cells contain 2 distinct populations including Gr-1 high CD11b + granulocytic (P7) and Gr-1 int CD11b + monocytic (P10) MDSC subsets. ( b–c ) Biopanning with Ph.D.-12 peptide phage display library on Gr-1 and CD11b labeled splenocytes showed enriched phage eluted from sorted MDSC subsets. Biopanning enrichment was expressed in either “Number of plaques / 10 6 cells” or phage “Output / Input ratio” (× 10 –8 ). ( d ) Binding of synthetic FITC-conjugated G3 and H6 peptides on Gr-1 + CD11b + gated MDSC from EL4-bearing C57BL/6 mice ( n = 4), compared with Gr-1 − CD11b − gated non-MDSC splenocytes. A non-specific peptide (irrel peptide) was used as a negative control to exclude non-specific binding. The data are representative of 3 identical experiments.

    Techniques Used: Binding Assay, Mouse Assay, Labeling, Negative Control

    12) Product Images from "Peptidic inhibitors of insulin-degrading enzyme with potential for dermatological applications discovered via phage display"

    Article Title: Peptidic inhibitors of insulin-degrading enzyme with potential for dermatological applications discovered via phage display

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0193101

    Peptides derived by phage display. A , Peptide sequences deduced from DNA sequencing of 20 clones from the Ph.D.™-C7C library. B , Consensus sequence derived from analysis of all data. C , Parent peptides selected for synthesis and testing. C , D , Peptide sequences deduced from DNA sequencing of 39 clones from the Ph.D.™-12 library, conducted as two independent runs ( D and E ). Note that Seq-12A-07 did not yield a decipherable sequence. F , Parent peptides selected for subsequent synthesis and testing based on prevalence.
    Figure Legend Snippet: Peptides derived by phage display. A , Peptide sequences deduced from DNA sequencing of 20 clones from the Ph.D.™-C7C library. B , Consensus sequence derived from analysis of all data. C , Parent peptides selected for synthesis and testing. C , D , Peptide sequences deduced from DNA sequencing of 39 clones from the Ph.D.™-12 library, conducted as two independent runs ( D and E ). Note that Seq-12A-07 did not yield a decipherable sequence. F , Parent peptides selected for subsequent synthesis and testing based on prevalence.

    Techniques Used: Derivative Assay, DNA Sequencing, Clone Assay, Sequencing

    13) Product Images from "Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization"

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-02891-x

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.
    Figure Legend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Techniques Used: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay

    14) Product Images from "Identification of Fusarium virguliforme FvTox1-Interacting Synthetic Peptides for Enhancing Foliar Sudden Death Syndrome Resistance in Soybean"

    Article Title: Identification of Fusarium virguliforme FvTox1-Interacting Synthetic Peptides for Enhancing Foliar Sudden Death Syndrome Resistance in Soybean

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0145156

    Diagrammatic representation of the workflow applied in affinity purification of M13 phage clones that displayed FvTox1-interacting synthetic peptides. (A), Bio-panning of the phage display libraries on plastic surface of a microtiter plates coated with 1.5 ml FvTox1 (30 ng/μl). Unbound phage particles were washed off; and M13 phage particles bound to FvTox1 were used to infect E . coli for starting a second round of panning. The process was repeated once more. (B), Plating of candidate M13 phage clones displaying FvTox1-interacting peptides. An eluate from the last panning in A was plated on X-gal/IPTG agar plates. (C), Identification of candidate M13 phage clones displaying FvTox1-interacting peptides. Phage clones were adsorbed onto nitrocellulose paper and hybridized to the His-tagged purified FvTox1 proteins. FvTox1-interacting clones were identified by detecting FvTox1 with the anti-His antibody. (D), Western blot analysis of the selected phage clones for interaction with FvTox1. Selected M13 phage particles from plates in C were transferred to nitrocellulose filters and hybridized to FvTox1, which was detected with an anti-His antibody. (E), Western blot analysis of the selected clones for interaction with FvTox1. Selected clones in D were reinvestigated for interaction with FvTox1, adsorbed onto a nitrocellulose membranes and detecting the interaction of individual clones to FvTox1 with an anti-M13 antibody (Details are presented in S2 Fig ). (F), Electropherogram of a nucleotide molecule encoding an FvTox1-intearcting peptide is presented.
    Figure Legend Snippet: Diagrammatic representation of the workflow applied in affinity purification of M13 phage clones that displayed FvTox1-interacting synthetic peptides. (A), Bio-panning of the phage display libraries on plastic surface of a microtiter plates coated with 1.5 ml FvTox1 (30 ng/μl). Unbound phage particles were washed off; and M13 phage particles bound to FvTox1 were used to infect E . coli for starting a second round of panning. The process was repeated once more. (B), Plating of candidate M13 phage clones displaying FvTox1-interacting peptides. An eluate from the last panning in A was plated on X-gal/IPTG agar plates. (C), Identification of candidate M13 phage clones displaying FvTox1-interacting peptides. Phage clones were adsorbed onto nitrocellulose paper and hybridized to the His-tagged purified FvTox1 proteins. FvTox1-interacting clones were identified by detecting FvTox1 with the anti-His antibody. (D), Western blot analysis of the selected phage clones for interaction with FvTox1. Selected M13 phage particles from plates in C were transferred to nitrocellulose filters and hybridized to FvTox1, which was detected with an anti-His antibody. (E), Western blot analysis of the selected clones for interaction with FvTox1. Selected clones in D were reinvestigated for interaction with FvTox1, adsorbed onto a nitrocellulose membranes and detecting the interaction of individual clones to FvTox1 with an anti-M13 antibody (Details are presented in S2 Fig ). (F), Electropherogram of a nucleotide molecule encoding an FvTox1-intearcting peptide is presented.

    Techniques Used: Affinity Purification, Clone Assay, Purification, Western Blot

    15) Product Images from "Screening and selection of peptides specific for esophageal cancer cells from a phage display peptide library"

    Article Title: Screening and selection of peptides specific for esophageal cancer cells from a phage display peptide library

    Journal: Journal of Cardiothoracic Surgery

    doi: 10.1186/1749-8090-9-76

    Enrichment of phage achieved with each round of selection from a Ph. D.-12TM phage display peptide library using Eca109 cells. (A-C) Dilution of phage at 1:100 were plated for rounds 1 and 2, then a dilution of 1:1000 was plated for round 3.
    Figure Legend Snippet: Enrichment of phage achieved with each round of selection from a Ph. D.-12TM phage display peptide library using Eca109 cells. (A-C) Dilution of phage at 1:100 were plated for rounds 1 and 2, then a dilution of 1:1000 was plated for round 3.

    Techniques Used: Selection

    16) Product Images from "Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs"

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    Journal: Viruses

    doi: 10.3390/v12121360

    Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.
    Figure Legend Snippet: Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.

    Techniques Used: Sequencing

    Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.
    Figure Legend Snippet: Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .
    Figure Legend Snippet: Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.
    Figure Legend Snippet: Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.

    Techniques Used:

    Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .
    Figure Legend Snippet: Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .

    Techniques Used: Sequencing, Amplification, Stripping Membranes

    17) Product Images from "Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization"

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-02891-x

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.
    Figure Legend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Techniques Used: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay

    18) Product Images from "Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling"

    Article Title: Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2018.01.043

    Humoral immune response studied using the mimotope-variation analysis (MVA) method. A. Schematic drawing of the workflow in MVA. MVA is a high-throughput random peptide phage display analysis. A random peptide display library (PhD12) was used which contained 10^9 different 12-mer peptide sequences introduced to the N-terminus of the phage major coat protein pIII (NEB). For MVA, sample-specific IgG proteins (antibodies, Human IgG fraction ) present in human sera of interest are allowed to interact with the phage-displayed peptides and the IgG-phage complexes were captured to protein G magnetic beads, while the unbound phages were washed away ( Peptide library display ). Captured phages were lysed and DNA amplified with primer sequences containing a tag with a unique barcode sequence and the final amplicons were pooled for NGS analysis ( HTS sequencing ). The primer set homologous to the M13KE vector sequences that flank the random peptide coding sequence was used to amplify a 50-bp fragment. Data analysis to classify peptides that were specific to Pmdx-infected, -vaccinated and NT1-diseased individuals was carried out by comparing the profiles of peptides (mimotopes) from diseased to those from non-diseased ( Peptide profile analysis ). On average, MVA generated 1.8 million peptide sequences with unique structure (divergence) totaling 2.8 million peptide sequences in abundance (total abundance; number of reads) per sample. Altogether, a peptide data set with > 16 million sequences (Totpep) with unique structure was generated. B. Analysis of peptides revealed highly divergent patterns (immunoprofiles) across study cohorts. The fraction of top 2500 peptides with unique structure and highest values of abundance - reflecting the peaking immune reactivity of each sample - was analyzed for variance. Top2500 peptide dataset contained altogether 160,000 sequences out of which 121,142 were unique. Pie charts display the sequence distribution of unique peptides across all samples analyzed. The left pie ( blue ) displays the proportion of shared vs. unique peptides: ~86% were unique to one individual whereas ~14% of the peptide sequences were shared between samples, out of these ~8.5% were common to 2 samples, 5% to 3–10 samples and 0.5% were detected in > 10 samples. The right pie ( red ) displays the distribution of shared 16,844 peptide sequences out of which ~60.7% were common to 2 samples, 35.7% to 3–10 samples and 3.6% were seen in > 10 samples. The four pie charts (below) exemplify the peptide profile structures in different clinical cohorts. The size of each pie piece is proportional to the number of unique peptides common to one or more samples of a clinical cohort. Blue - represents unique peptides, red - the most shared. C. Individual variation in peptide divergence is characteristic to all immunoprofiles. Top 2500 peptides were analyzed to assess the range of individual peptide variation across study cohorts. Blue dots mark peptide divergence in a single sample. As indicated, between one to two thousand peptides were individual-specific, whilst the most common peptides (shared by > 10 individuals) ranged in divergence from tens to 350 across samples. Range of unique peptide variations was similar across all study samples. D. Heat map image of a random fragment of MVA profile encompassing 400 peptides across study samples. Peptide profiles were individual-specific with a highly varying abundance. Each column represents the peptide profile of a single individual, and each line represents a peptide with a unique primary structure. Abundance is presented as counts in logarithmic scale ( in log ); black colour depicts peptides captured at higher abundance, and white those at lower abundance. Shown are peptide profiles that were common to 3–10 individuals. Abbreviations: Abundance – peptide frequency; Divergence – all unique peptides; HC - healthy control; H1N1-HC – H1N1 infected; Pdmx-HC - Pandemrix-vaccinated; NT1 - narcolepsy type 1 (including 10 Pandemrix-induced NT1 samples).
    Figure Legend Snippet: Humoral immune response studied using the mimotope-variation analysis (MVA) method. A. Schematic drawing of the workflow in MVA. MVA is a high-throughput random peptide phage display analysis. A random peptide display library (PhD12) was used which contained 10^9 different 12-mer peptide sequences introduced to the N-terminus of the phage major coat protein pIII (NEB). For MVA, sample-specific IgG proteins (antibodies, Human IgG fraction ) present in human sera of interest are allowed to interact with the phage-displayed peptides and the IgG-phage complexes were captured to protein G magnetic beads, while the unbound phages were washed away ( Peptide library display ). Captured phages were lysed and DNA amplified with primer sequences containing a tag with a unique barcode sequence and the final amplicons were pooled for NGS analysis ( HTS sequencing ). The primer set homologous to the M13KE vector sequences that flank the random peptide coding sequence was used to amplify a 50-bp fragment. Data analysis to classify peptides that were specific to Pmdx-infected, -vaccinated and NT1-diseased individuals was carried out by comparing the profiles of peptides (mimotopes) from diseased to those from non-diseased ( Peptide profile analysis ). On average, MVA generated 1.8 million peptide sequences with unique structure (divergence) totaling 2.8 million peptide sequences in abundance (total abundance; number of reads) per sample. Altogether, a peptide data set with > 16 million sequences (Totpep) with unique structure was generated. B. Analysis of peptides revealed highly divergent patterns (immunoprofiles) across study cohorts. The fraction of top 2500 peptides with unique structure and highest values of abundance - reflecting the peaking immune reactivity of each sample - was analyzed for variance. Top2500 peptide dataset contained altogether 160,000 sequences out of which 121,142 were unique. Pie charts display the sequence distribution of unique peptides across all samples analyzed. The left pie ( blue ) displays the proportion of shared vs. unique peptides: ~86% were unique to one individual whereas ~14% of the peptide sequences were shared between samples, out of these ~8.5% were common to 2 samples, 5% to 3–10 samples and 0.5% were detected in > 10 samples. The right pie ( red ) displays the distribution of shared 16,844 peptide sequences out of which ~60.7% were common to 2 samples, 35.7% to 3–10 samples and 3.6% were seen in > 10 samples. The four pie charts (below) exemplify the peptide profile structures in different clinical cohorts. The size of each pie piece is proportional to the number of unique peptides common to one or more samples of a clinical cohort. Blue - represents unique peptides, red - the most shared. C. Individual variation in peptide divergence is characteristic to all immunoprofiles. Top 2500 peptides were analyzed to assess the range of individual peptide variation across study cohorts. Blue dots mark peptide divergence in a single sample. As indicated, between one to two thousand peptides were individual-specific, whilst the most common peptides (shared by > 10 individuals) ranged in divergence from tens to 350 across samples. Range of unique peptide variations was similar across all study samples. D. Heat map image of a random fragment of MVA profile encompassing 400 peptides across study samples. Peptide profiles were individual-specific with a highly varying abundance. Each column represents the peptide profile of a single individual, and each line represents a peptide with a unique primary structure. Abundance is presented as counts in logarithmic scale ( in log ); black colour depicts peptides captured at higher abundance, and white those at lower abundance. Shown are peptide profiles that were common to 3–10 individuals. Abbreviations: Abundance – peptide frequency; Divergence – all unique peptides; HC - healthy control; H1N1-HC – H1N1 infected; Pdmx-HC - Pandemrix-vaccinated; NT1 - narcolepsy type 1 (including 10 Pandemrix-induced NT1 samples).

    Techniques Used: High Throughput Screening Assay, Magnetic Beads, Amplification, Sequencing, Next-Generation Sequencing, Plasmid Preparation, Infection, Generated

    19) Product Images from "Targeting of Embryonic Stem Cells by Peptide-Conjugated Quantum Dots"

    Article Title: Targeting of Embryonic Stem Cells by Peptide-Conjugated Quantum Dots

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0012075

    Selection of Ph.D-12 phage pools against ES cells. (A) Subtraction efficiency with dES cells and PMEFs. The phage pool underwent three subtractions with dES cells and three subtractions with PMEFs in each round of biopanning. The efficiency is shown as the percentage of recovered phage numbers from subtraction to input phage numbers. (B) Selection efficiency with ES cells. The binding efficiency of phage pool is shown as the percentage of eluted phage numbers to input phage numbers in each round of biopanning. (C) Alignment of peptide sequences displayed by monoclonal M13 phages selected binding to ES cells. Identical sequences are shown in color. (D) Affinity and specificity of purified candidate M13 phages binding to indicated cell types using ELISA. The peptides displayed by selected phages are APWHLSSQYSRT, GYPHPWTLWHLN, LDVRPWYVTPLP, TPLINMNALTVT, and WAPEKDYMQLMK. The first three amino acid letters of these sequences are used to stand for the corresponding phages. Results are presented as absorption value (mean ± standard derivation) in ELISA assay. Each experiment was repeated three times independently. **: p
    Figure Legend Snippet: Selection of Ph.D-12 phage pools against ES cells. (A) Subtraction efficiency with dES cells and PMEFs. The phage pool underwent three subtractions with dES cells and three subtractions with PMEFs in each round of biopanning. The efficiency is shown as the percentage of recovered phage numbers from subtraction to input phage numbers. (B) Selection efficiency with ES cells. The binding efficiency of phage pool is shown as the percentage of eluted phage numbers to input phage numbers in each round of biopanning. (C) Alignment of peptide sequences displayed by monoclonal M13 phages selected binding to ES cells. Identical sequences are shown in color. (D) Affinity and specificity of purified candidate M13 phages binding to indicated cell types using ELISA. The peptides displayed by selected phages are APWHLSSQYSRT, GYPHPWTLWHLN, LDVRPWYVTPLP, TPLINMNALTVT, and WAPEKDYMQLMK. The first three amino acid letters of these sequences are used to stand for the corresponding phages. Results are presented as absorption value (mean ± standard derivation) in ELISA assay. Each experiment was repeated three times independently. **: p

    Techniques Used: Selection, Binding Assay, Purification, Enzyme-linked Immunosorbent Assay

    Related Articles

    Incubation:

    Article Title: Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run
    Article Snippet: .. The antibodies and phages from the PhD.-12 library were incubated overnight on a rotator at 4 °C. ..

    Article Title: Discovery of Small Anti‐ACE2 Peptides to Inhibit SARS‐CoV‐2 Infectivity
    Article Snippet: .. The first well was blocked with BSA (2%) for 2 h, followed by incubation with 2019‐nCov Spike Protein RBD (500 ng) (catalog# 40592‐V05H, Sino Biological, Wayne, PA) for 2 h. The Ph.D.‐12 Phage Display Peptide Library (catalog # E81102, New England BioLabs, Ipswich, MA) was added to the first well and incubated at room temperature for 1 h. Unbound phages from the first well were then transferred to the second well and incubated for 1 h. The bound phages were eluted and amplified for the next round of biopanning. ..

    Binding Assay:

    Article Title: Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run
    Article Snippet: .. Screening the Antibodies’ Binding Peptides The Ph.D-12 phage display library was purchased from New England Biolabs. ..

    Amplification:

    Article Title: Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run
    Article Snippet: .. According to the protocol, the amplified Ph.D-12 phage display library was purified, titered, and stored at −20 °C in 50% glycerin. ..

    Article Title: Discovery of Small Anti‐ACE2 Peptides to Inhibit SARS‐CoV‐2 Infectivity
    Article Snippet: .. The first well was blocked with BSA (2%) for 2 h, followed by incubation with 2019‐nCov Spike Protein RBD (500 ng) (catalog# 40592‐V05H, Sino Biological, Wayne, PA) for 2 h. The Ph.D.‐12 Phage Display Peptide Library (catalog # E81102, New England BioLabs, Ipswich, MA) was added to the first well and incubated at room temperature for 1 h. Unbound phages from the first well were then transferred to the second well and incubated for 1 h. The bound phages were eluted and amplified for the next round of biopanning. ..

    Purification:

    Article Title: Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run
    Article Snippet: .. According to the protocol, the amplified Ph.D-12 phage display library was purified, titered, and stored at −20 °C in 50% glycerin. ..

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    New England Biolabs ph d 12 peptide library aliquot
    Screening and identification of FRα binding peptides. A <t>Ph.D.-12</t> phage library was used to screen FRα binding phages with four rounds of biopanning. ( A ) The enrichment of FRα binding phages were evaluated by phage recovery yields of each round selection. ( B ) Polyclonal phage ELISA using elutes after each round selection. ( C ) 94 phage clones were randomLy picked from the third round selection, and their binding affinities for FRα were analyzed individually by phage ELISA.
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    Screening and identification of FRα binding peptides. A Ph.D.-12 phage library was used to screen FRα binding phages with four rounds of biopanning. ( A ) The enrichment of FRα binding phages were evaluated by phage recovery yields of each round selection. ( B ) Polyclonal phage ELISA using elutes after each round selection. ( C ) 94 phage clones were randomLy picked from the third round selection, and their binding affinities for FRα were analyzed individually by phage ELISA.

    Journal: Scientific Reports

    Article Title: Identification of a peptide for folate receptor alpha by phage display and its tumor targeting activity in ovary cancer xenograft

    doi: 10.1038/s41598-018-26683-z

    Figure Lengend Snippet: Screening and identification of FRα binding peptides. A Ph.D.-12 phage library was used to screen FRα binding phages with four rounds of biopanning. ( A ) The enrichment of FRα binding phages were evaluated by phage recovery yields of each round selection. ( B ) Polyclonal phage ELISA using elutes after each round selection. ( C ) 94 phage clones were randomLy picked from the third round selection, and their binding affinities for FRα were analyzed individually by phage ELISA.

    Article Snippet: After washing 3 times with TBS containing 0.05% (v/v) Tween 20 (TBST), 100 μL Ph.D.-12 peptide library aliquot (New England Biolabs, Inc., USA) containing 1011 phages was added to each well and the plate was incubated for 1 hour at 37 °C.

    Techniques: Binding Assay, Selection, Enzyme-linked Immunosorbent Assay, Clone Assay

    Identification of novel epitopes in GBM proteins recognized by eluted anti-GBM autoantibodies using random phage display peptide library. ( A ) Western blot screening of phage clones for their surface protein p III that positively reacted to GBM autoantibodies. Phage clones were from repeated panning by anti-GBM autoantibodies. ( B ) Confirmation of a representative clone that displayed positive reactivity to anti-GBM autoantibodies but not rat IgG by Western blot. Only one positive and one negative clone are shown. Note that the positive clone reacted to the Ab but not rat IgG. ( C ) Phylogeny tree for DNA sequences of 36 bp inserts from clones in which their pIII reacted to anti-GBM autoantibodies. Four clusters, indicated as A, B, C and D, are shown. ( D ) Comparison of a.a. sequences of GBM proteins with those deduced from A, B, C and D. Highlighted (yellow) letters indicate the identical residues or motif. Underlined letters are the identified a.a. sequences of GBM proteins (shown at the left) with their positions noted as superscript numbers. Flank a.a. residues were added for synthesis of 15-mer peptides as shown at the right.

    Journal: PLoS ONE

    Article Title: Inter-molecular epitope spreading does not lead to extension of autoimmunity beyond target tissue in autoimmune glomerulonephritis

    doi: 10.1371/journal.pone.0202988

    Figure Lengend Snippet: Identification of novel epitopes in GBM proteins recognized by eluted anti-GBM autoantibodies using random phage display peptide library. ( A ) Western blot screening of phage clones for their surface protein p III that positively reacted to GBM autoantibodies. Phage clones were from repeated panning by anti-GBM autoantibodies. ( B ) Confirmation of a representative clone that displayed positive reactivity to anti-GBM autoantibodies but not rat IgG by Western blot. Only one positive and one negative clone are shown. Note that the positive clone reacted to the Ab but not rat IgG. ( C ) Phylogeny tree for DNA sequences of 36 bp inserts from clones in which their pIII reacted to anti-GBM autoantibodies. Four clusters, indicated as A, B, C and D, are shown. ( D ) Comparison of a.a. sequences of GBM proteins with those deduced from A, B, C and D. Highlighted (yellow) letters indicate the identical residues or motif. Underlined letters are the identified a.a. sequences of GBM proteins (shown at the left) with their positions noted as superscript numbers. Flank a.a. residues were added for synthesis of 15-mer peptides as shown at the right.

    Article Snippet: Epitope mapping with a phage display random peptide library To identify epitopes recognized by the eluted anti-GBM autoantibody, a combinatorial library peptide (12-mers) phage display kit was utilized (Ph.D.™ 12mer Phage Display Library, New England Biolabs, MA) following manufacturer’s protocol for solution phase panning with affinity bead capture.

    Techniques: Western Blot, Clone Assay

    Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.

    Journal: Viruses

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    doi: 10.3390/v12121360

    Figure Lengend Snippet: Visualization of the percentage of motif-bearing sequences, in which a second motif can be found. The population of sequences to be compared is defined in the X-axis, motifs which are compared for their appearance in the respective population in the Y-axis. In red bars the number of sequences, carrying the motif is given, in green bars the number of reads of the sequences carrying the motif is given. Motif comparisons colored dark red show that these occur multiple times in the sequences, leading to percentages of > 100%. Calculations were performed with the sequence set of the naïve Ph.D. TM –12 library.

    Article Snippet: Occurrence of sequences carrying the motif SxHS in the randomized 12-mer displayed on the Ph.D.TM –12 phage library.

    Techniques: Sequencing

    Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.

    Journal: Viruses

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    doi: 10.3390/v12121360

    Figure Lengend Snippet: Sequence logos of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown are logos, calculated using pLogo [ 18 ] based on the significance of the individual residues in context to the naïve phage library Ph.D. TM –12 as background frequency. ( A ) Amplification of the naïve phage library ( B ) Elution and stripping fractions of three rounds of biopanning showing the enrichment of the consensus sequence FHMPLTDPGQVQ.

    Article Snippet: Occurrence of sequences carrying the motif SxHS in the randomized 12-mer displayed on the Ph.D.TM –12 phage library.

    Techniques: Sequencing, Amplification, Stripping Membranes

    Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .

    Journal: Viruses

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    doi: 10.3390/v12121360

    Figure Lengend Snippet: Comparison of the amino acid composition of selected fractions of three rounds of biopanning against on-column immobilized arsenic. Shown in heatmaps is the relative occurrence of each amino acid on each position of the randomized 12-mer peptide sequence, displayed on M13KE phage of the combinatorial Ph.D. TM –12 phage library (New England Biolabs, Ipswich, MA, USA) relative to the percentage of occurrence of the amino acids in the naïve library. The original amino acid percentage on each position of the naïve library is shown in ( A ). In ( B ) the relative occurrences of the following fractions are shown: amplification of the naïve library, input biopanning round 1 (BP1), elution and stripping biopanning round 3 (BP3). Figure A2 , which shows heatmaps of all fractions can be found in Appendix A .

    Article Snippet: Occurrence of sequences carrying the motif SxHS in the randomized 12-mer displayed on the Ph.D.TM –12 phage library.

    Techniques: Sequencing, Amplification, Stripping Membranes

    Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.

    Journal: Viruses

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    doi: 10.3390/v12121360

    Figure Lengend Snippet: Occurrence of sequences carrying the motif xxxxxxxxxQxQ with two carboxy-terminal glutamines on positions 10 and 12 of the randomized 12-mer display on the Ph.D. TM –12 phage library. The occurrence in reads (green) and sequences (red) of the respective fraction of three rounds of biopanning against on-column immobilized arsenic ( A ) and of the calculated core fractions ( B ) is shown.

    Article Snippet: Occurrence of sequences carrying the motif SxHS in the randomized 12-mer displayed on the Ph.D.TM –12 phage library.

    Techniques:

    Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .

    Journal: Viruses

    Article Title: Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

    doi: 10.3390/v12121360

    Figure Lengend Snippet: Sequence motif occurrence in reads (green), fractions of the three biopanning rounds (red, middle) and in the calculated core fractions (red, right). Motifs were calculated using MEME [ 19 ]. Shown are: the naïve Ph.D. TM –12 library, the amplification of the naïve library (naï. lib. amp.) and the pass of the preceding pre-panning (negative), which was used after amplification as input for the three rounds of biopanning against on-column immobilized arsenic. For the three biopanning rounds, the respective input, wash, elution and stripping fraction are shown as well as the core fractions calculated in Section 3.6 .

    Article Snippet: Occurrence of sequences carrying the motif SxHS in the randomized 12-mer displayed on the Ph.D.TM –12 phage library.

    Techniques: Sequencing, Amplification, Stripping Membranes

    Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Journal: Scientific Reports

    Article Title: Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization

    doi: 10.1038/s41598-017-02891-x

    Figure Lengend Snippet: Polystyrene binding of PB-TUP, Ph.D.-12 peptide library, M13KE, and a non-relevant phage clone (D12) determined by ELISA. Four phage clones were added to the microtiter plates and the wells were treated with six different blocking buffers (first line) and six different washing buffers (second line), separately. ELISA values were used to evaluate the binding ability of these four phage clones to polystyrene. NFM had the best blocking effect. PBST and TBST were more effective washing buffers than the others. PB-TUP phage clone always had much higher absorbance comparing with the other phage clones. The experiments were performed in triplicates and repeated twice.

    Article Snippet: 1010 pfu of possible polystyrene binding clone PB-TUP, Ph.D.-12 peptide library, M13KE (LacZa(-) wild-type M13 phage, New England BioLabs, Inc., USA), and a non-relevant phage D12 clone was added into the microtiter plates as a control group and the plates were incubated overnight at 4 °C.

    Techniques: Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Blocking Assay