ph d 7 peptide library kit  (New England Biolabs)


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    Structured Review

    New England Biolabs ph d 7 peptide library kit
    ( a ) Phage panning procedure. The <t>Ph.D.-7</t> phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds
    Ph D 7 Peptide Library Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ph d 7 peptide library kit/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ph d 7 peptide library kit - by Bioz Stars, 2022-05
    93/100 stars

    Images

    1) Product Images from "Peptide affinity reagents for AAV capsid recognition and purification"

    Article Title: Peptide affinity reagents for AAV capsid recognition and purification

    Journal: Gene therapy

    doi: 10.1038/gt.2011.46

    ( a ) Phage panning procedure. The Ph.D.-7 phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds
    Figure Legend Snippet: ( a ) Phage panning procedure. The Ph.D.-7 phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds

    Techniques Used: Incubation, Binding Assay, Amplification

    2) Product Images from "Specific Targeting of Hepatitis C Virus Core Protein by an Intracellular Single-Chain Antibody of Human Origin"

    Article Title: Specific Targeting of Hepatitis C Virus Core Protein by an Intracellular Single-Chain Antibody of Human Origin

    Journal:

    doi: 10.1002/hep.22366

    Identification of scFv42C binding motif in HCV core protein by multiple sequence alignment. Core protein sequence (residues 79–88) is shown on the top, followed by deduced amino acid sequences of eight phage clones (mimotopes) from the Ph.D.-7
    Figure Legend Snippet: Identification of scFv42C binding motif in HCV core protein by multiple sequence alignment. Core protein sequence (residues 79–88) is shown on the top, followed by deduced amino acid sequences of eight phage clones (mimotopes) from the Ph.D.-7

    Techniques Used: Binding Assay, Sequencing

    3) Product Images from "Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia"

    Article Title: Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2022.851096

    ELISPOT analysis. (A) IL-4 ELISPOT. The number of spots in experimental group 1 (PBMCs + peptide 1) was significantly higher than that in the negative control well. However, there was no difference in the number of spots in experimental group 2 (PBMCs + peptide 2) compared with the negative control well. (B) IFN-γ ELISPOT. There was no difference in the number of spots between the experimental well (PBMCs + positive peptide 1) and the negative control well.
    Figure Legend Snippet: ELISPOT analysis. (A) IL-4 ELISPOT. The number of spots in experimental group 1 (PBMCs + peptide 1) was significantly higher than that in the negative control well. However, there was no difference in the number of spots in experimental group 2 (PBMCs + peptide 2) compared with the negative control well. (B) IFN-γ ELISPOT. There was no difference in the number of spots between the experimental well (PBMCs + positive peptide 1) and the negative control well.

    Techniques Used: Enzyme-linked Immunospot, Negative Control

    (A) The purified antibody of normal controls (lane 2) and patients with untreated IRP (lane 4) assessed by SDS-PAGE. Lane 1, molecular weight markers. Lanes 3 and 5, only a small amount of antibody remained in the flow-through solution of normal controls (lane 3) and patients with untreated IRP (lane 5). (B) Phage biopanning and enrichment after three rounds.
    Figure Legend Snippet: (A) The purified antibody of normal controls (lane 2) and patients with untreated IRP (lane 4) assessed by SDS-PAGE. Lane 1, molecular weight markers. Lanes 3 and 5, only a small amount of antibody remained in the flow-through solution of normal controls (lane 3) and patients with untreated IRP (lane 5). (B) Phage biopanning and enrichment after three rounds.

    Techniques Used: Purification, SDS Page, Molecular Weight

    Peptide/HLA-DRB1*15:01 MHC class II tetramer staining for antigen-specific CD4 + T cells analyzed by flow cytometry. The top row plots show PBMCs from patients with untreated IRP (HLA-DRB1*15:01). The image in the middle row shows sample of cells from HLA-DRB1*15:01 normal controls. The bottom row figure shows cell samples from patients with untreated IRP (non–HLA-DRB1*15:01). All plots were derived by gating on CD3-postive and CD4-postive lymphocytes. The first four images in each row are the control group (no tetramer), and the last four ones are the experimental group with tetramer. In the upper right quadrant of the plot, there is a population of antigen-specific CD4 + T cells is visible from cells of patients with untreated IRP (HLA-DRB1*15:01) stained with PE-labeled ProT2 MHC tetramer compared to the control group (black arrows).
    Figure Legend Snippet: Peptide/HLA-DRB1*15:01 MHC class II tetramer staining for antigen-specific CD4 + T cells analyzed by flow cytometry. The top row plots show PBMCs from patients with untreated IRP (HLA-DRB1*15:01). The image in the middle row shows sample of cells from HLA-DRB1*15:01 normal controls. The bottom row figure shows cell samples from patients with untreated IRP (non–HLA-DRB1*15:01). All plots were derived by gating on CD3-postive and CD4-postive lymphocytes. The first four images in each row are the control group (no tetramer), and the last four ones are the experimental group with tetramer. In the upper right quadrant of the plot, there is a population of antigen-specific CD4 + T cells is visible from cells of patients with untreated IRP (HLA-DRB1*15:01) stained with PE-labeled ProT2 MHC tetramer compared to the control group (black arrows).

    Techniques Used: Staining, Flow Cytometry, Derivative Assay, Labeling

    4) Product Images from "A rationally designed mimotope library for profiling of the human IgM repertoire"

    Article Title: A rationally designed mimotope library for profiling of the human IgM repertoire

    Journal: bioRxiv

    doi: 10.1101/308973

    Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies; (B) sequence logo of the LO by position relative to the overall background frequencies; (C) sequence logo of the frequencies by position; (D) sequence logo of the LO by position in an amplified Ph.d.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med, 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ); (E) sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D). The skewing of the distribution in the free N-terminus appears to be property of the library while the selection by the IgM repertoire leads to slight skewing in the middle of the sequence towards negatively charged residues, glycine and tryptophan.
    Figure Legend Snippet: Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies; (B) sequence logo of the LO by position relative to the overall background frequencies; (C) sequence logo of the frequencies by position; (D) sequence logo of the LO by position in an amplified Ph.d.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med, 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ); (E) sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D). The skewing of the distribution in the free N-terminus appears to be property of the library while the selection by the IgM repertoire leads to slight skewing in the middle of the sequence towards negatively charged residues, glycine and tryptophan.

    Techniques Used: Sequencing, Amplification, Selection

    5) Product Images from "Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries"

    Article Title: Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2019.02796

    Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies. (B) Sequence logo of the LO by position relative to the overall background frequencies. (C) Sequence logo of the frequencies by position. (D) Sequence logo of the LO by position in an amplified Ph.D.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med , 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ). (E) Sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D) . The skewing of the distribution in the free N-terminus appears to be property of the library, whereas the selection by the IgM repertoire leads to slight skewing in the middle of the sequence toward negatively charged residues, glycine and tryptophan.
    Figure Legend Snippet: Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies. (B) Sequence logo of the LO by position relative to the overall background frequencies. (C) Sequence logo of the frequencies by position. (D) Sequence logo of the LO by position in an amplified Ph.D.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med , 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ). (E) Sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D) . The skewing of the distribution in the free N-terminus appears to be property of the library, whereas the selection by the IgM repertoire leads to slight skewing in the middle of the sequence toward negatively charged residues, glycine and tryptophan.

    Techniques Used: Sequencing, Amplification, Selection

    6) Product Images from "Amsacta moorei Entomopoxvirus Inhibitor of Apoptosis Suppresses Cell Death by Binding Grim and Hid"

    Article Title: Amsacta moorei Entomopoxvirus Inhibitor of Apoptosis Suppresses Cell Death by Binding Grim and Hid

    Journal: Journal of Virology

    doi: 10.1128/JVI.79.6.3684-3691.2005

    Phage display sequences identified after three rounds of phage selection and amplification. (A) Twenty representative isolates from the Ph.D.-7 library (New England BioLabs) were sequenced after each round. Recurrences of specific amino acids after the third round are indicated in parentheses. X, no significant recurrence. (B) The binding motif sequences of mammalian (human) and insect ( Drosophila ) IBM-containing proteins. The first seven amino acids of the mature forms of each protein are shown. Superscripted numbers indicate the amino acid positions of the alanine in the precursor proteins.
    Figure Legend Snippet: Phage display sequences identified after three rounds of phage selection and amplification. (A) Twenty representative isolates from the Ph.D.-7 library (New England BioLabs) were sequenced after each round. Recurrences of specific amino acids after the third round are indicated in parentheses. X, no significant recurrence. (B) The binding motif sequences of mammalian (human) and insect ( Drosophila ) IBM-containing proteins. The first seven amino acids of the mature forms of each protein are shown. Superscripted numbers indicate the amino acid positions of the alanine in the precursor proteins.

    Techniques Used: Selection, Amplification, Binding Assay

    7) Product Images from "Discovery of a novel small molecular peptide that disrupts helix 34 of bacterial ribosomal RNA †"

    Article Title: Discovery of a novel small molecular peptide that disrupts helix 34 of bacterial ribosomal RNA †

    Journal: RSC Advances

    doi: 10.1039/c9ra07812f

    (a) 16S helix 34 is a target for antibacterial agents. Perturbation of helix 34 structure can be lethal to bacteria. (b) Sequences and percentage occurrence (% O) of peptides selected that bind to target RNA at the end of third biopanning are shown. Blue, green, pink, grey, orange, and yellow colored fonts represent positively charged, polar, negatively-charged, aromatic hydrophobic, conformationally unique, and non-polar amino acids, respectively.
    Figure Legend Snippet: (a) 16S helix 34 is a target for antibacterial agents. Perturbation of helix 34 structure can be lethal to bacteria. (b) Sequences and percentage occurrence (% O) of peptides selected that bind to target RNA at the end of third biopanning are shown. Blue, green, pink, grey, orange, and yellow colored fonts represent positively charged, polar, negatively-charged, aromatic hydrophobic, conformationally unique, and non-polar amino acids, respectively.

    Techniques Used:

    (a) Changes in circular dichroism spectra of 3h34 RNA upon addition of P1 is shown. (b) Circular dichroism change at 266 nm wavelength also indicate two clear P1 binding events.
    Figure Legend Snippet: (a) Changes in circular dichroism spectra of 3h34 RNA upon addition of P1 is shown. (b) Circular dichroism change at 266 nm wavelength also indicate two clear P1 binding events.

    Techniques Used: Binding Assay

    (a) Predicted secondary structure of 3h34 model RNA is shown. (b) Schematic representation of RNA binding model of P1. The model assumes mutually exclusive binding of P1 close to either the methylation site or the hairpin loop. (c) The fraction of tryptophan fluorescence change is plotted against RNA concentrations used. Titration experiments are duplicated and results are averaged. (d) Equilibrium dissociation constants for various RNA–P1 complexes are obtained by least square fitting of titration curves to a modified binding isotherm equation. Top and bottom panels show K D s for lighter and tighter P1-RNA complexes, respectively. The 3h34F1 and 3h34F2 RNAs were fitted to the single binding isotherm.
    Figure Legend Snippet: (a) Predicted secondary structure of 3h34 model RNA is shown. (b) Schematic representation of RNA binding model of P1. The model assumes mutually exclusive binding of P1 close to either the methylation site or the hairpin loop. (c) The fraction of tryptophan fluorescence change is plotted against RNA concentrations used. Titration experiments are duplicated and results are averaged. (d) Equilibrium dissociation constants for various RNA–P1 complexes are obtained by least square fitting of titration curves to a modified binding isotherm equation. Top and bottom panels show K D s for lighter and tighter P1-RNA complexes, respectively. The 3h34F1 and 3h34F2 RNAs were fitted to the single binding isotherm.

    Techniques Used: RNA Binding Assay, Binding Assay, Methylation, Fluorescence, Titration, Modification

    8) Product Images from "Synthetic Toll Like Receptor-4 (TLR-4) Agonist Peptides as a Novel Class of Adjuvants"

    Article Title: Synthetic Toll Like Receptor-4 (TLR-4) Agonist Peptides as a Novel Class of Adjuvants

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0030839

    Identification of LPS specific peptide mimotopes. LPS antibody was immobilized at a concentration of 1 µg per well of a 96-well plate. Phages (2×10 11 ) expressing 7-mer peptides were initially added to the well of a 96-well plate containing immobilized LPS antibody after which non-specific phages were removed. Twelve random phage clones were selected from three rounds of panning and specificity to LPS antibody (black bars) was confirmed by ELISA using HSP70 antibody (white bars) as a negative control. All 12 (RS01-RS12) clones selected displayed specific reactivity to LPS antibody, as determined using the HRP labeled anti-M13 phage antibody which was detected by the HRP substrate SIGMAFAST™ OPD and absorbance measured at 490 nm. Each experiment was repeated three times with similar results observed and the standard deviation shown above each sample represents three replicates in one experiment.
    Figure Legend Snippet: Identification of LPS specific peptide mimotopes. LPS antibody was immobilized at a concentration of 1 µg per well of a 96-well plate. Phages (2×10 11 ) expressing 7-mer peptides were initially added to the well of a 96-well plate containing immobilized LPS antibody after which non-specific phages were removed. Twelve random phage clones were selected from three rounds of panning and specificity to LPS antibody (black bars) was confirmed by ELISA using HSP70 antibody (white bars) as a negative control. All 12 (RS01-RS12) clones selected displayed specific reactivity to LPS antibody, as determined using the HRP labeled anti-M13 phage antibody which was detected by the HRP substrate SIGMAFAST™ OPD and absorbance measured at 490 nm. Each experiment was repeated three times with similar results observed and the standard deviation shown above each sample represents three replicates in one experiment.

    Techniques Used: Concentration Assay, Expressing, Clone Assay, Enzyme-linked Immunosorbent Assay, Negative Control, Labeling, Standard Deviation

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    New England Biolabs ph d 7 peptide library kit
    ( a ) Phage panning procedure. The <t>Ph.D.-7</t> phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds
    Ph D 7 Peptide Library Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ph d 7 peptide library kit/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ph d 7 peptide library kit - by Bioz Stars, 2022-05
    93/100 stars
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    ( a ) Phage panning procedure. The Ph.D.-7 phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds

    Journal: Gene therapy

    Article Title: Peptide affinity reagents for AAV capsid recognition and purification

    doi: 10.1038/gt.2011.46

    Figure Lengend Snippet: ( a ) Phage panning procedure. The Ph.D.-7 phage display library was co-incubated with AAV capsids to allow binding (B), followed by washing (W) of unbound phage and elution (E) of bound phage. Bound phage were then amplified and subjected to three rounds

    Article Snippet: Phage panning studies were carried out using the Ph.D.-7 peptide library kit (New England Biolabs) with a diversity of ~1.2×109 linear heptapeptides as per manufacturer instructions.

    Techniques: Incubation, Binding Assay, Amplification

    Identification of scFv42C binding motif in HCV core protein by multiple sequence alignment. Core protein sequence (residues 79–88) is shown on the top, followed by deduced amino acid sequences of eight phage clones (mimotopes) from the Ph.D.-7

    Journal:

    Article Title: Specific Targeting of Hepatitis C Virus Core Protein by an Intracellular Single-Chain Antibody of Human Origin

    doi: 10.1002/hep.22366

    Figure Lengend Snippet: Identification of scFv42C binding motif in HCV core protein by multiple sequence alignment. Core protein sequence (residues 79–88) is shown on the top, followed by deduced amino acid sequences of eight phage clones (mimotopes) from the Ph.D.-7

    Article Snippet: To identify peptide sequences recognized by the scFv42C antibody, the Ph.D.-7 phage display library peptides kit containing linear peptides (randomly presenting 7–12 amino acids) (New England Biolabs) was used.

    Techniques: Binding Assay, Sequencing

    ELISPOT analysis. (A) IL-4 ELISPOT. The number of spots in experimental group 1 (PBMCs + peptide 1) was significantly higher than that in the negative control well. However, there was no difference in the number of spots in experimental group 2 (PBMCs + peptide 2) compared with the negative control well. (B) IFN-γ ELISPOT. There was no difference in the number of spots between the experimental well (PBMCs + positive peptide 1) and the negative control well.

    Journal: Frontiers in Immunology

    Article Title: Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia

    doi: 10.3389/fimmu.2022.851096

    Figure Lengend Snippet: ELISPOT analysis. (A) IL-4 ELISPOT. The number of spots in experimental group 1 (PBMCs + peptide 1) was significantly higher than that in the negative control well. However, there was no difference in the number of spots in experimental group 2 (PBMCs + peptide 2) compared with the negative control well. (B) IFN-γ ELISPOT. There was no difference in the number of spots between the experimental well (PBMCs + positive peptide 1) and the negative control well.

    Article Snippet: Then, we used phage-displayed random peptide library (Ph.D-7 Phage Display Peptide Library Kit, New England Biolabs) for biopanning according to the kit’s recommendations.

    Techniques: Enzyme-linked Immunospot, Negative Control

    (A) The purified antibody of normal controls (lane 2) and patients with untreated IRP (lane 4) assessed by SDS-PAGE. Lane 1, molecular weight markers. Lanes 3 and 5, only a small amount of antibody remained in the flow-through solution of normal controls (lane 3) and patients with untreated IRP (lane 5). (B) Phage biopanning and enrichment after three rounds.

    Journal: Frontiers in Immunology

    Article Title: Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia

    doi: 10.3389/fimmu.2022.851096

    Figure Lengend Snippet: (A) The purified antibody of normal controls (lane 2) and patients with untreated IRP (lane 4) assessed by SDS-PAGE. Lane 1, molecular weight markers. Lanes 3 and 5, only a small amount of antibody remained in the flow-through solution of normal controls (lane 3) and patients with untreated IRP (lane 5). (B) Phage biopanning and enrichment after three rounds.

    Article Snippet: Then, we used phage-displayed random peptide library (Ph.D-7 Phage Display Peptide Library Kit, New England Biolabs) for biopanning according to the kit’s recommendations.

    Techniques: Purification, SDS Page, Molecular Weight

    Peptide/HLA-DRB1*15:01 MHC class II tetramer staining for antigen-specific CD4 + T cells analyzed by flow cytometry. The top row plots show PBMCs from patients with untreated IRP (HLA-DRB1*15:01). The image in the middle row shows sample of cells from HLA-DRB1*15:01 normal controls. The bottom row figure shows cell samples from patients with untreated IRP (non–HLA-DRB1*15:01). All plots were derived by gating on CD3-postive and CD4-postive lymphocytes. The first four images in each row are the control group (no tetramer), and the last four ones are the experimental group with tetramer. In the upper right quadrant of the plot, there is a population of antigen-specific CD4 + T cells is visible from cells of patients with untreated IRP (HLA-DRB1*15:01) stained with PE-labeled ProT2 MHC tetramer compared to the control group (black arrows).

    Journal: Frontiers in Immunology

    Article Title: Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia

    doi: 10.3389/fimmu.2022.851096

    Figure Lengend Snippet: Peptide/HLA-DRB1*15:01 MHC class II tetramer staining for antigen-specific CD4 + T cells analyzed by flow cytometry. The top row plots show PBMCs from patients with untreated IRP (HLA-DRB1*15:01). The image in the middle row shows sample of cells from HLA-DRB1*15:01 normal controls. The bottom row figure shows cell samples from patients with untreated IRP (non–HLA-DRB1*15:01). All plots were derived by gating on CD3-postive and CD4-postive lymphocytes. The first four images in each row are the control group (no tetramer), and the last four ones are the experimental group with tetramer. In the upper right quadrant of the plot, there is a population of antigen-specific CD4 + T cells is visible from cells of patients with untreated IRP (HLA-DRB1*15:01) stained with PE-labeled ProT2 MHC tetramer compared to the control group (black arrows).

    Article Snippet: Then, we used phage-displayed random peptide library (Ph.D-7 Phage Display Peptide Library Kit, New England Biolabs) for biopanning according to the kit’s recommendations.

    Techniques: Staining, Flow Cytometry, Derivative Assay, Labeling

    Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies; (B) sequence logo of the LO by position relative to the overall background frequencies; (C) sequence logo of the frequencies by position; (D) sequence logo of the LO by position in an amplified Ph.d.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med, 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ); (E) sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D). The skewing of the distribution in the free N-terminus appears to be property of the library while the selection by the IgM repertoire leads to slight skewing in the middle of the sequence towards negatively charged residues, glycine and tryptophan.

    Journal: bioRxiv

    Article Title: A rationally designed mimotope library for profiling of the human IgM repertoire

    doi: 10.1101/308973

    Figure Lengend Snippet: Distribution of the amino acid residues in the mimotope library. (A) Log odds (LO) relative to background frequencies; (B) sequence logo of the LO by position relative to the overall background frequencies; (C) sequence logo of the frequencies by position; (D) sequence logo of the LO by position in an amplified Ph.d.-7 phage library without ligand selection relative to the overall background frequencies (based on W. L. Matochko, R. Derda. “Error analysis of deep sequencing of phage libraries: peptides censored in sequencing”. Comput Math Methods Med, 2013, 491612. 2013., http://www.chem.ualberta.ca/~derda/parasitepaper/rawfiles/PhD7-GAC-30FuR.txt ); (E) sequence logo of the LO by position relative to the frequencies by position in the amplified, unselected library shown in (D). The skewing of the distribution in the free N-terminus appears to be property of the library while the selection by the IgM repertoire leads to slight skewing in the middle of the sequence towards negatively charged residues, glycine and tryptophan.

    Article Snippet: A 7-mer random peptide library (E8100S, Ph.D. -7, New England Biolabs, USA) was panned overnight at 4°C on pooled human IgM adsorbed on polystyrene plates at a concentration of 0.1 mg/ml, washed, eluted with glycine buffer at pH 2.7 and immediately brought to pH7.

    Techniques: Sequencing, Amplification, Selection