Scientific Posters

Zymo Research's scientific posters highlight the latest breakthroughs in molecular biology, showcasing innovations spanning from epigenetics to microbiomics. We are proud to present insights from our collaborations with leading scientists and institutions worldwide, with more contributions to the field of life science on the horizon.

Use of Metagenomic Reference Materials to Benchmark and Optimize Lysis and Extraction Methods Against a Known Input
Michael M. Weinstein, Kristopher Locken, Brett Farthing, Elaine Wolfe, Shuiquan Tang, Venu Lagishetty, Jonathan P. Jacobs, Braden Tierney, Ryan Kemp, and Christopher Mason

This study introduces a quantitative framework using defined microbial reference standards and a novel Measurement Integrity Quotient (MIQ) to benchmark microbiome lysis and extraction methods, revealing substantial variability and bias across commonly used workflows. The findings demonstrate that optimized mechanical bead-based lysis is critical for accurate community representation, highlighting the importance of reproducible, quantitatively validated methodologies for ensuring reliable cross-study comparisons and biologically meaningful conclusions in microbiome research.

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Novel Spin Column Solution for Optimized Purification of Nucleic Acids from Heavily Inhibited Samples for Highly Accurate Sequencing and PCR Analysis
Ana Barrionuevo, Zoë Hermsen, Erica Carrasco, Xiaoxiao Cheng, Joshua Lee & Aaron Clausen

Accurate DNA sequencing analysis is essential for pathogen detection & understanding complex environmental microbiomes. However, polymerase chain reaction (PCR) and next-generation sequencing (NGS) performance can be severely compromised by the presence of PCR inhibitors, such as polyphenolic compounds. These inhibitors, including humic acids, are common in environmental samples and can co-purify with nucleic acids during extraction. Their presence disrupts enzymatic reactions, reduces amplification efficiency, and often results in costly re-runs or false-negative results. In this study, we evaluated a simple, single-step centrifugation-based spin column system for the removal of common PCR inhibitors from soil & wastewater samples. First, DNA was spiked with either humic acid or a PCR inhibitor cocktail containing bile salts, indigo, and hematin, then processed through the inhibitor removal column. Inhibitor removal and DNA recovery of the flow-through was quantified using spectrophotometry and fluorometry. Additionally, quantitative PCR was performed to evaluate DNA amplification before and after column treatment. Next, performance of this inhibitor removal technology was assessed with DNA extracted from soil and wastewater samples using commercially available DNA extraction kits. Results showed that the column removed > 96% of PCR inhibitors present without significant DNA loss. Additionally, quantitative PCR analysis demonstrated that amplification failed or was reduced in untreated soil & wastewater samples but was fully restored following treatment with the inhibitor removal column. Furthermore, 16S rRNA sequencing revealed that untreated DNA extracted from soil was too inhibited for identifying bacteria, whereas column treatment restored bacteria detection. These results demonstrate that polyphenolic compounds can significantly inhibit PCR and NGS-based analyses, and that this novel PCR inhibitor removal technology removes these inhibitors without compromising nucleic acid yield, effectively enhancing amplification sensitivity and analytical accuracy. Overall, this study underscores the importance of optimizing nucleic acid purification from inhibitor-rich environmental samples to ensure reliable downstream sequencing & microbial detection.

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A Sustainable, End-to-End Workflow for Wastewater Pathogen Surveillance
A. Damerum, J. Liu, W. Ullmer, M. Yang, E. Carrasco, X. Chen, E. Chen, A. Clausen, R. Yancey, A. Balasubramanian, J. Bhasin, K. Locken, K. Booher

Zymo's end-to-end wastewater workflow addresses the core challenges of wastewater surveillance – variability, inhibition, throughput and data interpretation – through standardized tools at each step: WSB for safer, simpler collection; automated co-purification for flexible downstream use; a deliberate choice of PCR or sequencing assays depending on the surveillance objective; and a no-install web portal for rapid data visualization and reporting.

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A Novel Workflow for Ultra-Short cfDNA Fragmentomics and Multiomic Profiling in Liquid Biopsies
Madison Valle, Duang Ratanachan, Kaitlyn Lee, Eunice Choi, Mingda Jin, Neeti Swarup, Irene Choi, Xiaojing Yang, David T. Wong &, Hanjun Kim

Liquid biopsy matrices—including plasma, serum, saliva, and urine—are increasingly used for non-invasive cancer detection, companion diagnostics, and recurrence monitoring. However, conventional column-based purification and double-stranded DNA library preparation fail to capture the full cfDNA landscape, particularly ultra-short fragments and single-stranded DNA (ssDNA). We evaluated a novel nucleic acid purification method paired with an ssDNA-compatible library preparation workflow to enable more comprehensive cfDNA profiling, using plasma samples as model systems.

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A Fully Automated Workflow for High-Throughput Purification of Transfection-Grade Plasmid
Joshua Lee, Zoë Hermsen & Aaron Clausen

Transfecting mammalian cells with plasmid DNA has become a critical tool for studying biological processes, developing therapeutics, gene editing, producing proteins, and generating recombinant viruses. While advances in DNA synthesis have simplified the construction of variant gene libraries for evaluating candidates of interest with transfection, purifying transfection-grade plasmid remains a major bottleneck for high-throughput screening. Traditionally, plasmid that meets the quantity, concentration, and low endotoxin requirements for mammalian cell transfection is prepared from large volumes of overnight E. coli culture using slow gravity flow anion-exchange columns and lengthy alcohol precipitation steps, making the process poorly suited for high-throughput and automated processing. To address this issue, Zymo Research developed a patented DNA purification method that is capable of purifying high amounts of transfection-grade plasmid from small volumes of overnight culture using silica coated magnetic beads. When combining this method with specialized magnetic particles that efficiently remove cellular debris following lysate neutralization, there is no need for centrifugation, making the plasmid purification process easy to completely automate using commercially available liquid handlers.

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