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positive controls  (Zymo Research)


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    Structured Review

    Zymo Research positive controls
    Positive Controls, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 892 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/positive+controls/ZymoBIOMICS+Microbial+Community+Standard/pmc12954305-58-4-10
    Average 99 stars, based on 892 article reviews
    positive controls - by Bioz Stars, 2026-09
    99/100 stars

    Images

    Related Articles

    Extraction:

    Article Title: Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.
    Article Snippet: Each sample swab and the associated buffer were thawed and transferred to Bashing Bead lysis tubes (Zymo Research, Irvine, CA, USA) containing a mixture of 0.1 mm and 0.5 mm-sized beads. .. To validate the assay, three positive controls (75 μL ZymoBIOMICS Microbial Community Standard in 725 μL DNA/RNA Shield, Zymo Research) and three negative controls (800 μL of DNA/RNA Shield, Zymo Research) were included in the extraction. .. Mechanical lysis was performed using a FastPrep24 5G bead beater (MP Biomedicals, Santa Ana, CA, USA).

    Article Title: Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment
    Article Snippet: Each sample swab and the associated buffer were thawed and transferred to Bashing Bead lysis tubes (Zymo Research, Irvine, CA, USA) containing a mixture of 0.1 mm and 0.5 mm-sized beads. .. To validate the assay, three positive controls (75 μL ZymoBIOMICS Microbial Community Standard in 725 μL DNA/RNA Shield, Zymo Research) and three negative controls (800 μL of DNA/RNA Shield, Zymo Research) were included in the extraction. .. Mechanical lysis was performed using a FastPrep24 5G bead beater (MP Biomedicals, Santa Ana, CA, USA).

    Negative Control:

    Article Title: Cryptic Insect Microbiome Compositions Unveiled with Full-Length 16S Sequencing
    Article Snippet: .. Negative control wells and positive controls (Zymo Research, Irvine, CA, USA) were sequenced along with samples. .. Samples were amplified using primers designed for PacBio Kinnex PCR (Pacific Biosciences, Menlo Park, CA, USA).

    Real-time Polymerase Chain Reaction:

    Article Title: Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.
    Article Snippet: .. Negative controls (blank filters and no template controls) and positive controls (ZymoBIOMICS Microbial Community DNA Standard [Zymo; D6305]) were included in each qPCR assay. ..

    Article Title: Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis
    Article Snippet: .. Negative controls (blank filters and no template controls) and positive controls (ZymoBIOMICS Microbial Community DNA Standard [Zymo; D6305]) were included in each qPCR assay. ..

    Polymerase Chain Reaction:

    Article Title: Effect of Operational Parameters on Dark Fermentative Hydrogen Production and Volatile Fatty Acids from Agro-Industrial By-Products
    Article Snippet: Thermal cycling consisted of an initial denaturation at 95 ◦C for 3 min, followed by 25 cycles of 95 ◦C for 30 s, 50 ◦C for 30 s and 72 ◦C for 30 s, with a final extension at 72 ◦C for 5 min. Amplicons were purified with AMPure XP beads (Beckman Coulter, Brea, CA, USA) and used as templates for an index PCR (8 cycles) to attach dual indices and Illumina adapters. .. Positive controls (ZymoBIOMICS Microbial Community DNA Standard, Zymo Research, Irvine, CA, USA) and negative controls (PCR-grade water) were processed in parallel to monitor amplification performance and potential contamination. .. Indexed libraries were purified, quantified with a Qubit dsDNA HS Assay (Thermo Fisher Scientific, Waltham, MA, USA), pooled in equimolar amounts and sequenced on an Illumina NextSeq 2000 (San Diego, CA, USA) platform using paired-end 2 × 300 bp chemistry. https://doi.org/10.3390/fermentation12020099 Raw paired-end reads were quality-checked with FastQC and processed in QIIME 2 (version 2024.5.0) using the DADA2 plugin for quality filtering, denoising, paired-end merging and chimera removal.

    Amplification:

    Article Title: Effect of Operational Parameters on Dark Fermentative Hydrogen Production and Volatile Fatty Acids from Agro-Industrial By-Products
    Article Snippet: Thermal cycling consisted of an initial denaturation at 95 ◦C for 3 min, followed by 25 cycles of 95 ◦C for 30 s, 50 ◦C for 30 s and 72 ◦C for 30 s, with a final extension at 72 ◦C for 5 min. Amplicons were purified with AMPure XP beads (Beckman Coulter, Brea, CA, USA) and used as templates for an index PCR (8 cycles) to attach dual indices and Illumina adapters. .. Positive controls (ZymoBIOMICS Microbial Community DNA Standard, Zymo Research, Irvine, CA, USA) and negative controls (PCR-grade water) were processed in parallel to monitor amplification performance and potential contamination. .. Indexed libraries were purified, quantified with a Qubit dsDNA HS Assay (Thermo Fisher Scientific, Waltham, MA, USA), pooled in equimolar amounts and sequenced on an Illumina NextSeq 2000 (San Diego, CA, USA) platform using paired-end 2 × 300 bp chemistry. https://doi.org/10.3390/fermentation12020099 Raw paired-end reads were quality-checked with FastQC and processed in QIIME 2 (version 2024.5.0) using the DADA2 plugin for quality filtering, denoising, paired-end merging and chimera removal.



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    Image Search Results


    Clusters of IL17A experimentally validated hits.

    Journal: bioRxiv

    Article Title: Overcoming the accuracy–generalization tradeoff in docking and scoring for prospective virtual screening

    doi: 10.64898/2026.08.03.742480

    Figure Lengend Snippet: Clusters of IL17A experimentally validated hits.

    Article Snippet: LY3509754 (MedChemExpress, HY-139206) was used as a positive-control IL17A inhibitor.

    Techniques:

    Prospective virtual screening campaigns were conducted against four therapeutically relevant targets representing distinct target classes and binding-site architectures. CD73 (nucleotidase), IRAK4 (kinase), and Factor XI (FXIa protease) were targeted through orthosteric inhibition, whereas IL-17A, a protein–protein interaction (PPI) target, was targeted through an allosteric binding site. For each target, the experimentally determined hit rate, a representative validated hit, its biochemical potency ( IC 50), and its structural similarity to the closest previously reported inhibitor (ECFP4 Tanimoto coefficient) are shown. The prospective campaigns identified 56 active compounds from 183 tested for CD73, 19 from 127 for IRAK4, 13 from 299 for Factor XI, and 6 from 194 for IL-17A. Across all four targets, representative hits exhibited low structural similarity to known inhibitors (ECFP4 Tanimoto coefficients of 0.22–0.27), demonstrating the ability of the virtual screening workflow to prospectively identify chemically novel scaffolds across both conventional orthosteric targets and more challenging protein–protein interaction targets.

    Journal: bioRxiv

    Article Title: Overcoming the accuracy–generalization tradeoff in docking and scoring for prospective virtual screening

    doi: 10.64898/2026.08.03.742480

    Figure Lengend Snippet: Prospective virtual screening campaigns were conducted against four therapeutically relevant targets representing distinct target classes and binding-site architectures. CD73 (nucleotidase), IRAK4 (kinase), and Factor XI (FXIa protease) were targeted through orthosteric inhibition, whereas IL-17A, a protein–protein interaction (PPI) target, was targeted through an allosteric binding site. For each target, the experimentally determined hit rate, a representative validated hit, its biochemical potency ( IC 50), and its structural similarity to the closest previously reported inhibitor (ECFP4 Tanimoto coefficient) are shown. The prospective campaigns identified 56 active compounds from 183 tested for CD73, 19 from 127 for IRAK4, 13 from 299 for Factor XI, and 6 from 194 for IL-17A. Across all four targets, representative hits exhibited low structural similarity to known inhibitors (ECFP4 Tanimoto coefficients of 0.22–0.27), demonstrating the ability of the virtual screening workflow to prospectively identify chemically novel scaffolds across both conventional orthosteric targets and more challenging protein–protein interaction targets.

    Article Snippet: Zimlovisertib (MedChemExpress, HY-19836) was used as a positive-control IRAK4 inhibitor.

    Techniques: Binding Assay, Inhibition

    (a) Prospective virtual screening workflow. Approximately 80 billion compounds from Enamine REAL Space were computationally screened and progressively prioritized to 153 compounds for procurement, of which 127 were experimentally evaluated. The number of compounds remaining after each filtering stage and the corresponding biochemical and cellular hit rates are shown. (b) Characterization of validated hits. Top, single-concentration biochemical inhibition measured at 100 and 10 μM . Middle, molecular weight (MW) and topological polar surface area (TPSA) distributions of validated hits. Bottom left, UMAP projection of ECFP4 fingerprints comparing validated hits (orange) with previously reported IRAK4 inhibitors (blue). Bottom right, distribution of ECFP4 Tanimoto similarity between validated hits and the closest known IRAK4 inhibitor, illustrating the chemical novelty of the identified compounds. (c) Representative validated IRAK4 inhibitors. Chemical structures, biochemical and cellular IC 50 values, physicochemical properties, and representative dose-response curves for two non-nucleotide inhibitors.

    Journal: bioRxiv

    Article Title: Overcoming the accuracy–generalization tradeoff in docking and scoring for prospective virtual screening

    doi: 10.64898/2026.08.03.742480

    Figure Lengend Snippet: (a) Prospective virtual screening workflow. Approximately 80 billion compounds from Enamine REAL Space were computationally screened and progressively prioritized to 153 compounds for procurement, of which 127 were experimentally evaluated. The number of compounds remaining after each filtering stage and the corresponding biochemical and cellular hit rates are shown. (b) Characterization of validated hits. Top, single-concentration biochemical inhibition measured at 100 and 10 μM . Middle, molecular weight (MW) and topological polar surface area (TPSA) distributions of validated hits. Bottom left, UMAP projection of ECFP4 fingerprints comparing validated hits (orange) with previously reported IRAK4 inhibitors (blue). Bottom right, distribution of ECFP4 Tanimoto similarity between validated hits and the closest known IRAK4 inhibitor, illustrating the chemical novelty of the identified compounds. (c) Representative validated IRAK4 inhibitors. Chemical structures, biochemical and cellular IC 50 values, physicochemical properties, and representative dose-response curves for two non-nucleotide inhibitors.

    Article Snippet: Zimlovisertib (MedChemExpress, HY-19836) was used as a positive-control IRAK4 inhibitor.

    Techniques: Concentration Assay, Inhibition, Molecular Weight