Author: Jordan Nutting

Improved FFPE Tissue Sample Processing with High-Throughput Automated DNA Extraction

Posted on by Jordan Nutting

In oncology, tissue biopsies are commonly fixed in formalin and embedded in paraffin (FFPE). These FFPE samples can be used with immunohistochemical or molecular analysis for identifying biomarkers that guide the diagnosis and therapeutic management of patients. This fixation technique allows long-term storage of samples but impacts the integrity of nucleic acids. This makes extracting DNA and RNA from FFPE tissues in sufficient quantity and quality for molecular analysis techniques such as NGS analyses challenging for molecular oncology laboratories.

“At Rennes University Hospital, we receive many lung cancer samples with little material available, or samples of poor quality. The nucleic acid extraction step is therefore critical to get good yield. We have seen that it had a direct impact on the success of downstream analysis,” said Dr. Alexandra Lespagnol. Lespagnol is the Technical Manager of the Molecular Genetics of Cancer core lab at the University Hospital of Rennes in France.

In order to accommodate the increasing number of samples that needed to be analyzed, the Molecular Genetics of Cancer core lab of the University Hospital of Rennes initiated an automation project for extracting DNA from FFPE tissues. The lab also wanted to improve sample tracking and reproducibility of their results.

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CCNE1-Amplified Cancers Targeted Through Synthetic Lethality Involving PKMYT1 Kinase

Posted on by Jordan Nutting

For cancers that have proven challenging to target with traditional therapies, one emerging option is an approach called synthetic lethality. Synthetic lethality arises when inactivation of two gene products together lead to cell death but where inactivation of one does not (1, 2). Targeting a gene that is synthetic lethal to a cancer-related mutation creates an opening to specifically kill cancer cells while leaving healthy cells untouched.

In a recent study in Nature, scientists found that cells with amplification of CCNE1 are sensitive to inhibition of PKYMT1 kinase and identified a small molecule that is a selective inhibitor of PKYMT1 (3). When mice with tumor xenografts derived from CCNE1­-high cell lines were dosed with the drug, researchers observed significantly slower tumor growth, and in some cases where the drug was co-dosed with another chemotherapeutic, tumor growth was completely halted.

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The Human Cell Atlas: Mapping a Cellular Landscape

Posted on by Jordan Nutting

From macrophages that seek out and destroy infectious agents to fibroblasts that hold tissues and organs together, cells give form and function to our bodies. However, despite their foundational roles in our biology, there is still much we don’t know about cells—like where different cell types are localized, what states a given cell type may take on, how the molecular characteristics of cells change over a person’s lifetime and more. Addressing these questions will provide a deeper understanding about the cellular and genetic basis of human health and disease.

Image contains several cells with a hazy outline of a DNA molecule in the background and one cell is highlighted
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Why Bring Automated Nucleic Acid Extraction into Your Lab?

Posted on by Jordan Nutting
Researcher adds sample try for an automated nucleic acid extraction robotics platform

Nucleic acid extraction is a time-consuming, resource-intensive process, but it doesn’t have to be. Automated systems are becoming more and more accessible and often can be operated with simple “plug and play” kits, freeing valuable resources

With these systems increasingly within reach, perhaps you’re thinking about introducing automated nucleic acid extraction into your lab. As you consider your options, here’s eight reasons why we think you should automate your nucleic extraction workflows.

8 Reasons to Automate Nucleic Acid Extraction in Your Lab:

1. Reach your project milestones and publish faster.

In the fast-paced, competitive environment of research and technology development, efficiency is key to reaching project milestones and publishing your work. Managing your resources effectively–especially time–can help you reach those goals.

Time spent on manual nucleic acid extractions is time lost on parallel work, which cuts down productivity. Automation is not only often faster than manual preparations, but it also frees your team to do more valuable hands-on work. 

As an example, the Maxwell® RSC cuts 40 minutes of hands-on-time per 16 samples. As the number of samples scales to 96 and beyond, liquid handlers like the Hamilton Star or Tecan Fluent can save many hours of hands-on-time per day.

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April is Sexual Assault Awareness Month

Posted on by Jordan Nutting

In the United States, April is a time to promote awareness about sexual assault and other forms of sexual violence. Sexual violence is a worldwide, pervasive problem that affects every one of us. By raising awareness, we can learn how to cultivate safe workplaces, homes, online platforms and other spaces, to prevent sexual violence and provide support for survivors.

In honor of Sexual Assault Awareness Month (SAAM), here are some of the key facts and figures about sexual violence gathered from the Rape, Abuse & Incest National Network (RAINN). Take a few minutes to read and learn more about this issue as SAAM draws to a close.

Teal memorial ribbons for sexual assault awareness month
Image Credit: National Sexual Violence Resource Center (NSVRC)
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Avian Influenza H5N1: What You Should Know About the Current US Outbreak

Posted on by Jordan Nutting

As a lifelong Midwesterner, I’m accustomed to the short-lived, false springs of January and February. I know to save gleeful cries of “spring is here!” until the trees bud and I can hear the buzzing trill of red-winged blackbirds and the calls of other birds returning from their winter homes. But this spring, the return of birdsong is not all good news.

In January 2022, the state of South Carolina reported a case of highly pathogenic avian influenza in a wild bird—the first detected case of this virus subtype in the United States since 2016. Since then, the outbreak has spread. Two weeks ago my home state of Wisconsin reported its first case in a commercial chicken flock of nearly 3 million birds, one of the largest US flocks affected so far.

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Antibody Correlates of Protection for mRNA Vaccine

Posted on by Jordan Nutting
Identifying correlates of protection, or biological markers that correlate with a certain level of protection from disease helps public health experts assess vaccination performance. Picture of a COVID-19 vaccine vial.

In the rapidly shifting context of a pandemic, public health officials need a way to quickly assess how vaccinations perform in changing situations. One approach is to identify correlates of protection, or biological markers that correlate with a certain level of protection from disease. This tool is used to assess the design and formulation of annual influenza vaccines, as immune system markers that correlate with protection from flu can give developers a sense of how effective the vaccine might be for different population groups. Though they are not a replacement for rigorous clinical trials, correlates of protection can provide meaningful and predictive data for vaccine developers with smaller trial sizes and less time.

A study published in November 2021 indicated that levels of binding antibodies and neutralizing antibodies for the SARS-CoV-2 virus in blood serum are correlates of protection for Moderna, Inc.’s COVE phase 3 clinical trial of their mRNA COVID-19 vaccine.

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Promega Ibérica Partnership Helps Students See Careers in Biotech

Posted on by Jordan Nutting

Graduate students often struggle to envision careers outside of the academic world. A partnership between Promega Ibérica and the Universidad Autónoma de Madrid (UAM) is helping change that for students in UAM’s Cellular Dynamics and Biomolecules master’s degree program.

María Jurado Pueyo, an application support manager with Promega Ibérica’s technical services department, leads a lab session on protein:protein interactions at the Universidad Autónoma de Madrid. As a part of the course students can explore careers in biotech.
María Jurado Pueyo, an application support manager with Promega Ibérica’s technical services department, leads a lab session on protein:protein interactions at the Universidad Autónoma de Madrid.
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Making Sense of Climate Change

Posted on by Jordan Nutting

Earlier this year, I had an opportunity to attend a virtual talk presented by leading climate scientist and communicator Dr. Katharine Hayhoe. She began by asking the audience to send in one word that describes how they feel when thinking about climate change. The responses popped up live in a word cloud on Hayhoe’s shared screen:

Anxious

Frozen

ARGHH!

Those words also describe how I felt when I realized the conclusion to my series of blogs on the 2021 Nobel Prizes would address the topic of climate change.

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Feeling Festive with Ion Channels

Posted on by Jordan Nutting

The tight embrace of welcoming hugs, the cozy warmth of a crackling fireplace, the brisk chill of afternoon walks in snowy woods—these are some of the feelings that, for me, make the winter holidays one of the best times of the year. This season, I’m also choosing to be thankful for the biology that makes these sensations possible.

This year’s Nobel Prize in Physiology and Medicine went to two scientists who discovered the receptors that allow us to sense touch and temperature. Joining other sensory mechanisms recognized by the Nobel committee, these discoveries add to our knowledge of how we interact with the world around us.

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