Journal: Journal of Cerebral Blood Flow & Metabolism

Article Title: Concentration, distribution, and influence of aging on the 18 kDa translocator protein in human brain: Implications for brain imaging studies

doi: 10.1177/0271678X19858003

Figure Lengend Snippet: Antibody and recombinant protein sources and conditions used.

Article Snippet: Abnova H00000706-M01 Mouse IgG 1k (3D8-B2) Unknown NA No major band identified Santa Cruz Biotech Sc-20120 rPolyAb (FL-169) Unknown NA No major band identified GFAP (50,48,45,and 43 kDa) Chemicon/Millipore MAB360 Mouse IgG 1 Unknown 1:100K Vimentin (57 kDa) Santa Cruz Biotech Sc-6260 Mouse IgG 1 Unknown 1:2K 2 nd antibodies Anti-rabbit IgG-HRP Southern Biotech 4050-05 Goat IgG 1:10-20K Anti-mouse IgG1-HRP Southern Biotech 1070-05 Goat IgG 1:10K Anti-goat IgG-HRP Southern Biotech 6160-05 Rabbit IgG 1:10K Recombinant TSPO Human TSPO, N-His Creative BioMart TSPO-3462H / / 0.1 ng 21 kDa Human TSPO, N-His/GST Creative BioMart TSPO-1696H / / <1 ng 48.8 kDa (crude lysate) Human TSPO, C-Myc/DDK Origene TP320107 / / 40 ng 23 kDa Mouse TSPO, N-His Jean J. Lacapere Gift / / 1 ng 21 kDa Mouse TSPO, C-Myc/DDK Origene TP605624 / / NA 23 kDa Rat TSPO, C-Myc/DDK Origene TP605625 / / NA 23 kDa Open in a separate window Antibody and recombinant protein sources and conditions used.

Techniques: Recombinant

Journal: bioRxiv

Article Title: Use of Epivolve phage display to generate a monoclonal antibody with opsonic activity directed against a subdominant epitope on extracellular loop 4 of Treponema pallidum BamA (TP0326)

doi: 10.1101/2023.05.13.540667

Figure Lengend Snippet: A peptide incorporating a non-native amino acid at a desired site is used to pan a scFv phage library for peptide binders. Phages that bind the modified, but not the native, peptide undergo AXM mutagenesis to generate phages that recognize the native peptide +/-the modified peptide with high affinity.

Article Snippet: The template plasmid for all phage display libraries is a derivative of the phagemid pIT2 ( ) with a human single-chain variable fragment Ab (scFv) fused to the coat protein III of bacteriophage M13, constructed at and kindly supplied by AxioMx Inc., an Abcam Company (“Abcam”).

Techniques: Modification, Mutagenesis

Journal: PLoS ONE

Article Title: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

doi: 10.1371/journal.pone.0007002

Figure Lengend Snippet: Equal amounts of bacterial lysates were separated by polyacrylamide gel electrophoresis and stained with Sypro Ruby (Pierce). Three independent clones for each variant were measured. Variant names are indicated above the gel lanes. Also shown are molecular weight standards (M); negative control samples (C); BSA mass standards (Stds). Red arrows indicate positions of full-length phi29 DNA polymerase (top panel) or scFv (bottom panel). BSA standard lanes include 500, 250, 125, 62.5, and 25 ng total protein (top panel, left to right) or 1000, 500, 250, 125, and 50 ng total protein (bottom panel, left to right).

Article Snippet: Two genes were chosen as targets for systematic exploration of the effect of synonymous codon usage on expression; one encoding the DNA polymerase of Bacillus phage Φ29 , the second encoding a synthetic single-chain antibody fragment (scFv) developed by OncoMed, Redwood City, CA.

Techniques: Polyacrylamide Gel Electrophoresis, Staining, Clone Assay, Variant Assay, Molecular Weight, Negative Control

Journal: PLoS ONE

Article Title: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

doi: 10.1371/journal.pone.0007002

Figure Lengend Snippet: For each variant the measured expression level was plotted against the expression predicted from a PLS model using genetic algorithm-selected codons. (A) Model fit for polymerase variant expression data. Blue diamonds indicate the 34 gene training set used to create the model. (B) Model fit for scFv expression data. Blue diamonds indicate the 24 gene training set used to create the model. Green triangles are variants from the initial set with undetectable expression, and which were not used for model building. (C) Combined model constructed from polymerase variants (34 red squares) and scFv variants (27 blue diamonds). Expression in each set was normalized to the highest expression level in that set ( = 3). R 2 (CV) indicates the correlation coefficient for the fit of the model in cross-validation (see ). Variants used to provide datapoints for construction of the models are indicated in .

Article Snippet: Two genes were chosen as targets for systematic exploration of the effect of synonymous codon usage on expression; one encoding the DNA polymerase of Bacillus phage Φ29 , the second encoding a synthetic single-chain antibody fragment (scFv) developed by OncoMed, Redwood City, CA.

Techniques: Variant Assay, Expressing, Construct, Biomarker Discovery

Journal: PLoS ONE

Article Title: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

doi: 10.1371/journal.pone.0007002

Figure Lengend Snippet: The codon adaptation index (part A) and the strength of mRNA secondary structure from position −4 to +38 relative to the initiating AUG (part B) were calculated for each variant synthesized in this study and plotted against the expression level measured for that variant. Blue diamonds indicate scFv variants. Red squares indicate polymerase variants. Expression levels are normalized to highest expressing variant for each set (equal to 3).

Article Snippet: Two genes were chosen as targets for systematic exploration of the effect of synonymous codon usage on expression; one encoding the DNA polymerase of Bacillus phage Φ29 , the second encoding a synthetic single-chain antibody fragment (scFv) developed by OncoMed, Redwood City, CA.

Techniques: Variant Assay, Synthesized, Expressing

Journal: PLoS ONE

Article Title: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

doi: 10.1371/journal.pone.0007002

Figure Lengend Snippet: For each scFv variant the measured expression level was plotted against the expression predicted from a PLS model using genetic algorithm-selected codons. Blue diamonds indicate the 24 gene training set used to create the model, Green triangles are variants from the initial set with undetectable expression. Red squares are new variants created by combining the first segment (the first 15 codons) of variant A1 with the remainder of these 6 poorly-expressed variants. Arrows indicate changes in predicted and measured expression upon 5′ codon exchange. Variants represented as green triangles or red squares were not included in the training set from which the model was built. Variant A1_11_11, in which a larger 43 codon portion of the 5′ section of the A11 gene was replaced with that of A1, is also indicated for comparison.

Article Snippet: Two genes were chosen as targets for systematic exploration of the effect of synonymous codon usage on expression; one encoding the DNA polymerase of Bacillus phage Φ29 , the second encoding a synthetic single-chain antibody fragment (scFv) developed by OncoMed, Redwood City, CA.

Techniques: Variant Assay, Expressing, Comparison

Journal: PLoS ONE

Article Title: Design Parameters to Control Synthetic Gene Expression in Escherichia coli

doi: 10.1371/journal.pone.0007002

Figure Lengend Snippet: For each variant the measured expression level was plotted against the expression predicted from a PLS model using genetic algorithm-selected codons. Polymerase variants (34 red squares) and scFv variants (27 blue diamonds) were included in the training set, expression in each set was normalized to the highest expression level in that set ( = 3). Green triangles show measured and predicted expression of 5 new genes not included in the training set. Correlation coefficients represent fits of the entire training set.

Article Snippet: Two genes were chosen as targets for systematic exploration of the effect of synonymous codon usage on expression; one encoding the DNA polymerase of Bacillus phage Φ29 , the second encoding a synthetic single-chain antibody fragment (scFv) developed by OncoMed, Redwood City, CA.

Techniques: Variant Assay, Expressing