Tips and Tools

Cell-Based Target Engagement and Functional Assays for NLRP3 Inhibitor Profiling Help Identify Successes and Failures

Posted on by Kari Kenefick

Identifying Inflammasome Inhibitors: What’s Missing
The NLRP3 inflammasome is implicated in a wide range of diseases. The ability to inhibit this protein complex could provide more precise, targeted relief to inflammatory disease sufferers than current broad-spectrum anti-inflammatory compounds, potentially without side effects.

Studies of NLRP3 inflammasome inhibitors have relied on cell-free assays using purified NLRP3. But cell-free assays cannot assess physical engagement of the inhibitor and target in the cellular micro-environment. Cell-free assays cannot show if an NLRP3 inhibitor enters the cell, binds the target and how long the inhibitor binding lasts.

Cell-based assays that interrogate the physical interaction of the NLRP3 target and inhibitor inside cells are needed.

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Raising Frogs Takes a Village: Accelerating Amphibian Research at the Marine Biological Laboratory

Posted on by Jordan Villanueva
Sally Seraphin and her students Maliah Ryan (second from right) and Jude Altman (right) work with a Promega Applications Scientist at the Marine Biological Laboratory

Sally Seraphin’s life in the research lab started with rats and roseate terns. Chimpanzees and rhesus macaques came next, then humans (and a brief foray into voles). When she pivoted to red-eyed tree frogs, Sally once again had to learn all kinds of new techniques. Suddenly, in addition to new sample prep and analysis techniques, she needed to get up to speed on amphibian care and husbandry. That led her to the Marine Biological Laboratory (MBL) in Woods Hole, MA.

“It’s a seaside resort atmosphere with experts in every technology you can imagine,” Sally says. “It’s a place to incubate and birth new approaches to answering questions.”

Sally spent the past two summers at MBL learning everything she needed to know about breeding and caring for amphibians. During that time, she also worked closely with Applications Scientists from Promega who helped her start extracting RNA from frog samples.

“The hands-on support from industry scientists is definitely unique to Promega and MBL,” she says. “It’s rare to have a specialist on hand who can help you learn, troubleshoot and optimize in such a finite amount of time.”

Adopting a New Model Organism

Sally uses red-eyed tree frogs to study early stress and developmental timing.
Sally uses red-eyed tree frogs to study early stress and developmental timing. Photo from Wikimedia.

Sally studies how early stress impacts brain and behavior development. She hopes to deepen our understanding of how adverse childhood experiences connect to mental illness and bodily disease later in life. In the past, she studied how factors such as parental absence affected the neurotransmission of dopamine in primates. Recently, she changed her focus to developmental timing.  

“Girls who are exposed to early trauma like sexual or physical abuse will sometimes reach puberty earlier than girls who aren’t,” Sally explains. “And I noticed that there are many species that will alter their developmental timing in response to predators or social and ecological threats.”

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Designing Science: A Behind-the-Scenes Look at Our Recent Journal Cover Art

Posted on by Jordan Nutting
A 3D illustration showing RAF inhibitor LXH254 engages BRAF or CRAF protomers (orange), but spares ARAF (red). Unoccupied ARAF is competent to trigger downstream mitogenic signaling, which is demonstrated with lightning bolts. Red cells in the background are fluorescently labeled RAS proteins, expressed in live cells. The Cell Chemical Biology cover type superimposes the image.
Image adapted from original artwork by iSO-FORM LLC.

We made the cover! Of Cell Chemical Biology, that is.

This July, Cell Chemical Biology editors accepted a study from Promega scientists and invited the research team to submit cover art for the issue. The study in question details a BRET-based method to quantify drug-target occupancy within RAF-KRAS complexes in live cells. Promega scientists Matt Robers and Jim Vasta collaborated with one of our talented designers, Michael Stormberg, to craft an image that accurately represents the science in a dynamic and engaging way.

You can check out the paper and cover art in the November 16 issue of Cell Chemical Biology.

I spoke with Michael Stormberg to learn more about the creative process that went into creating this cover art and how he worked with the research team and other collaborators.

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Can AI Help You Develop a Research Proposal?

Posted on by Jordan Nutting

Integrating artificial intelligence (AI) into the process of scientific research offers a wealth of efficiency-boosting tools that are transforming the ways scientists can approach their work. Many are already using AI to refine code, automate data processing, and edit papers, presentations, abstracts and more. Personally, I find generative language models like ChatGPT to be invaluable “editorial assistants” in my work as a science writer, helping me work through wonky sentence structures, be more concise and get over writer’s block, to name a few applications.

An AI-generated image of a man in a white lab coat who has a thoughtful look on his face. He is looking off camera with his hand on his chin. The background is a field of light bursts and bright lines against a dark backdrop.
Image generated using Adobe Firefly

But a scientist’s work doesn’t only involve writing or analyzing data, making presentations or keeping up with the literature. An essential component of any research scientist’s skillset is their ability to develop entirely new ideas and novel research proposals. Coming up with research questions and plans is a central component of graduate education and research careers, both in academia and industry.

As AI continues to advance and find broader use, a critical question arises: Can AI play a pivotal role in the creative process of developing entirely new ideas, such as crafting novel research proposals?

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Small RNA Transfection: How Small Players Can Make a Big Impact

Posted on by Simon Moe

When looking at small aspects of living things, especially cells, it can often be difficult to fully grasp the magnitude of regulation employed within them. We first learn the central dogma in high school biology. This is the core concept that DNA makes RNA and RNA makes protein. Despite this early education, it can be lost on many the biological methods that are employed to regulate this process. This regulation is very important when one considers the disastrous things that can occur when this process goes askew, such as cancer, or dysregulated cell death. Therefor it is very important to understand how these regulatory mechanisms work and employ tools to better understand them.

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Promega qPCR Grant Series #3: Immunotherapy Researcher, Dr. Sabrina Alves dos Reis 

Posted on by Anna Bennett
Professional headshot image of Dr. Sabrina Alves dos Reis, subject of the blog post
Sabrina Alves dos Reis

In our third and final installment of the Promega qPCR Grant Recipient blog series, we highlight Dr. Sabrina Alves dos Reis, a trained immunotherapy researcher. Her work has focused on developing tools for more accessible cancer therapies using CAR-T cells. Here, we explore Dr. Alves dos Reis’ academic and scientific journeys, highlight influential mentorship and foreshadow her plans for the Promega qPCR grant funds. 

Dr. Alves dos Reis’ career began with a strong affinity for biology. As an undergraduate student, she pursued a degree in biological science, where she developed a foundational understanding for designing and developing research projects. As her passion for science heightened, she decided to continue her journey in science, culminating in a PhD at the Fundação Oswaldo Cruz Institute in Rio de Janeiro, Brazil. Her research projects focused on the unexplored territory of adipose tissue as a site for Mycobacterium leprae—or leprosy bacillus—infection. She mentioned that this work piqued her curiosity for improving immunotherapies and laid the foundation for her future in cancer research.  

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Elevate Your Research: Exploring the Power of 8-Dye STR Chemistry with the Spectrum Compact CE System

Posted on by Promega

In genetic research, staying at the forefront of technology is crucial. The latest breakthrough in human identification comes in the form of 8-dye Short Tandem Repeat (STR) chemistry. This innovation promises unprecedented precision and accuracy in DNA analysis, revolutionizing the way we approach genetic studies. In this blog post, we’ll delve into the world of 8-color chemistry and explore how it seamlessly integrates with the game-changing Spectrum Compact CE System.

Understanding 8-Dye STR Chemistry

The introduction of 8-dye chemistry expands the capability of STR analysis, enabling researchers to analyze more DNA markers with smaller amplicons, providing more robust data from degraded or inhibited DNA samples.  The performance of the 8-color dye chemistries from Promega on the Spectrum Compact CE System is sensitive, with both chemsitries (PowerPlex® 35 GY System and the upcoming PowerPlex® 18 E System) producing 100% profiles from their suggested inputs down to as little as 62.5 pg of DNA. The 18E system produced 100% profiles down to 31.25 pg of input DNA with minimal signal bleed through and low system noise.

Table showing percent STR profiles generated with decreasing input DNA using the PowerPlex 35GY or PowerPlex 18 E chemistry on the Spectrum Compact CE System
Table showing percent profiles generated with decreasing input DNA using the PowerPlex® 35GY or PowerPlex® 18E chemistry on the Spectrum Compact CE System.
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Promega qPCR Grant Series #2: Molecular Biologist, Laura Leighton

Posted on by Anna Bennett

Our second installment of the Promega qPCR Grant Recipient blog series highlights Dr. Laura Leighton, a trained molecular biologist and postdoctoral researcher at the Australian Institute for Bioengineering and Nanotechnology. Leighton’s scientific journey features a passion for molecular biology and problem-solving. Her path has been illuminated by mentorship, relationships with fellow scientists and a commitment to creativity in overcoming challenges. Here, we explore her scientific journey, reflect on research lessons and foreshadow her plans for the Promega qPCR grant funds.

Dr. Laura Leighton grew up in a rural area in Far North Queensland, Australia, where she spent her early life exploring critters on the family farm. Her upbringing was infused with a deep connection to the environment, from raising tadpoles in wading pools to observing wildlife and witnessing food grow firsthand. Observing the biology around her ultimately piqued her interest in science from a young age. She then began her academic journey in 2011 at the University of Queensland, Australia. She studied biology while participating in a program for future researchers, which led her to undergraduate research work in several research labs.  She dabbled in many research avenues in order to narrow in on her scientific interests all while adding different research tools to her repertoire.

After serving as a research assistant in Dr. Timothy Bredy’s lab, she decided to continue work in this lab and pursue a PhD in molecular biology. During her PhD, Leighton worked on several projects from cephalopod mRNA interference to neurological wiring in mice. The common thread in these projects is Leighton’s passion for the puzzles of molecular biology:

“I also love molecular engineering and the modularity of molecular parts. There’s something really special about stringing together sequence in a DNA editor, then seeing it come to life in a cell,” she says.

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RAF Inhibitors: Quantifying Drug-Target Occupancy at Active RAS-RAF Complexes in Live Cells

Posted on by Ken Doyle

Mitogen-activated protein kinases (MAPKs) are a large family of proteins that regulate diverse cellular functions in eukaryotes, including gene expression, proliferation, differentiation and apoptosis (1). MAPK signaling pathways typically include three sequentially activated kinases, and these pathways are triggered in response to extracellular stimuli, such as cytokines, mitogens, growth factors and oxidative stress (1). Ultimately, the signal is transmitted to the nucleus, with the activation of a specific transcription factor that modulates the expression of one or more genes.

Among MAPK pathways, the RAS-RAF-MEK-ERK signaling pathway has been studied extensively. Mutations in RAS family proteins and resultant dysregulation of the signaling pathway are implicated in a variety of cancers. Therefore, this pathway is a popular target for anticancer drug development.

An overview of the RAS-RAF-MEK-ERK signaling pathway.
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Promega qPCR Grant Series #1: Marine Plant Ecologist, Dr. Agustín Moreira-Saporiti

Posted on by Anna Bennett
Dr. Agustín Moreira-Saporiti is a postdoctoral researcher at the Marine Biological Laboratory and is studying flowering processes in marine seagrass

Marine seagrasses are submerged flowering plants that form essential underwater meadows, fostering diverse ecosystems and providing a habitat for marine life. Our first Promega qPCR Grant winner and marine ecologist, Dr. Agustín Moreira-Saporiti, plans to continue adding to a fascinating body of work aimed at understanding flowering in marine seagrasses.

Dr. Moreira-Saporiti began his journey into marine plant ecology at the University of Vigo, Spain, where he earned a bachelor’s degree in marine sciences. He then went on to complete a master’s degree at the University of Bremen (Germany) where his thesis focused the ecology of seagrasses in Zanzibar, Tanzania. His passion for marine botany led him down a deeper exploration of marine plants, unraveling the intricate web of ecosystem processes within seagrasses.

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