#PromegaWorks

Descriptions of Promega products in action from examples of Promega products in the peer-reviewed literature to technical tips on how to address common laboratory and experimental questions

Promega qPCR Grant Funds Genetic Database for Antarctic Krill

Posted on by AnnaKay Kruger

Boasting a biomass of roughly 400 million tons, Antarctic krill are a key source of food for a wide array of marine life, including sea birds, seals, penguins and whales. As with the rest of the oceanic ecosystem, krill are subject to rapidly shifting climate conditions, prompting scientists to seek a deeper understanding of how they might adapt to a changing environment.

Facing a general lack of genetic information on the species, Professors Cristiano De Pittà and Gabriele Sales from the Department of Biology at the University of Padova in Italy set out to define the krill transcriptome, or sequences of ribonucleic acid (RNA), and in doing so facilitated the discovery of key gene sequences that may play important roles in krill reproduction and survival.

In recent years, there have been concerns about potential impacts to the krill population from ocean warming and commercial fishing operations. Mapping the krill transcriptome may offer scientists crucial insight into the effects of climate change and anthropogenic activity on the dynamics of the Antarctic ecosystem. Doing so is no small feat. Though krill may be miniscule, their genome is 15 times the size of the human genome.

To this end, the research groups of De Pittà and Sales established the database KrillDB, providing a single resource where scientists can access a comprehensive catalogue of krill genes and RNA transcripts. This database represented a powerful bioinformatic tool for examining molecular processes in krill. Funded in part by the Promega 2019 qPCR Grant Program, researchers subsequently rolled out an updated database, KrillDB2, which includes improvements to the quality and breadth of the sequences covered and the information associated. Their corresponding study, published summer 2022 in Scientific Reports, identified a series of genes involved in the krill molting cycle, the reproductive process and sexual maturation, and included never-before reported insights into the expression of microRNA precursors and their effect on krill physiology.

The 2019 Promega qPCR Grant Program offered recipients $10,000 in free PCR reagents and related products, as well as access to Promega technical services and training teams. 

Researcher and awardee Alberto Biscontin said of the grant’s impact on their project: “RNA sequencing approaches allow us to determine the level of expression of thousands of genes with a single experiment. The standard in the field is to define transcript expression levels by quantitative RT-PCR to technically validate RNA-seq results. We have been relying on the GoTaq® qPCR solutions by Promega for years.” He added, “We have used the GoTaq® 1-Step RT-qPCR System to compare the level of expression of candidate genes with those obtained from RNA-seq analysis. This allowed us to verify at any time the reliability of our bioinformatics pipelines.”

In the future, researchers plan to maintain the KrillDB2 database with the latest genome and transcriptome sequencing data, to provide the most comprehensive integrative analysis possible. They intend to develop a multi-crustaceans database to support future comparative genomics studies. The KrillDB2 database may also serve as a model to develop other databases for similar species.

Learn more about the GoTaq® 1-Step RT-qPCR System.

Read more about the 2019 qPCR Grant winners.  

We’re committed to supporting scientists who are using molecular biology to make a difference. Learn more about our qPCR Grant program.  

Related Posts

Kornberg Innovation Seminars: Inspiring Creativity in Promega R&D

Posted on by Jordan Villanueva
Kornberg Center was designed to accelerate scientific exploration.

“Are you going to the talk?”

The refrain regularly echoes through the halls of every academic lab building. During our education, we’re treated to a non-stop supply of speakers on every subject we can imagine. Prestigious speaker series gave us chances to hear from some of the world’s most prominent experts on subjects that would shape scientific pursuits for the next decade and beyond. When we leave academia, however, it can be difficult to find those same opportunities to learn. Sure, there are lab meetings and conferences, but when can you be treated to a renowned expert giving a talk just down the hall?

Promega Head of Biology Frank Fan aimed to address that problem when he developed a plan for the Kornberg Innovation Seminars (KIS), a recurring speaker series to be held in the new home for Promega R&D. Kornberg Center is an environment where Promega scientists are challenged to think outside-the-box and anticipate the challenges life science researchers will be facing tomorrow. Frank believed that opportunities to learn from a wide variety of guest experts would be critical for inspiring that type of thinking.

“Promega R&D focuses on understanding scientists’ needs and providing novel solutions,” Frank says. “The KIS program is about helping us achieve that vision.”

Continue reading “Kornberg Innovation Seminars: Inspiring Creativity in Promega R&D”

3D Cell Culture Models: Challenges for Cell-Based Assays

Posted on by Isobel Maciver
3D Cell Culture Spheroid
3D Cell Culture Spheroid

In 3D cell culture models, cells are grown under conditions that allow the formation of multicellular spheroids or microtissues. Instead of growing in a monolayer on a plate surface, cells in 3D culture grow within a support matrix that allows them to interact with each other, forming cell:cell connections and creating an environment that mimics the situation in the body more closely than traditional 2D systems. Although 3D cultures are designed to offer a more physiologically accurate environment, the added complexity of that environment can also present challenges to experimental design when performing cell-based assays. For example, it can be a challenge for assay reagents to penetrate to the center of larger microtissues and for lytic assays to disrupt all cells within the 3D system.

Earlier this week Terry Riss, a Senior Product Specialist at Promega, presented a Webinar on the challenges of performing cell-based assays on microtissues in 3D cell culture. During the Webinar, Terry gave an overview of the different methods available for 3D cell culture, providing a description of the advantages of each. He then discussed considerations for designing and optimizing cell-based  assays for use in 3D culture systems, providing several  recommendations to keep in mind when performing cell viability assays on larger microtissue samples.

Continue reading “3D Cell Culture Models: Challenges for Cell-Based Assays”

NAD: A Renaissance Molecule and its Role in Cell Health

Posted on by Kari Kenefick

NAD is a pyridine nucleotide. It provides the oxidation and reduction power for generation of ATP by mitochondria. For many years it was believed that the primary function of NAD/NADH in cells was to harness and transfer energy  from glucose, fatty and amino acids through pathways like glycolysis, beta-oxidation and the citric acid cycle.

Promega NAD/NADH-Glo system and how to prepare samples for identification of NAD or NADH.
Promega NAD/NADH-Glo system and how to prepare samples for identification of NAD or NADH.

However NAD also is recognized as an important cell signaling molecule and substrate. The many regulatory pathways now known to use NAD+ in signaling include multiple aspects of cellular homeostasis, energy metabolism, lifespan regulation, apoptosis, DNA repair and telomere maintenance.

This resurrection of NAD importance is due in no small part to the discovery of NAD-using enzymes, especially the sirtuins.

Continue reading “NAD: A Renaissance Molecule and its Role in Cell Health”

Measuring Changing Metabolism in Cancer Cells

Posted on by Isobel Maciver

Because of the central role of energy metabolism in health and disease, and its effect on other cellular processes, assays to monitor changes in cellular metabolic state have wide application in both basic research and drug discovery. In the webinar “Tools for Cell Metabolism: Bioluminescent NAD(P)/NAD(P)H-Glo™ Assays” Jolanta Vidurigiene, a Senior Research Scientist at Promega, introduces three metabolism assays for measuring oxidized and reduced forms of NAD and NADP.

In this webinar, Jolanta provides background information on why it is important to be able to accurately measure metabolites such as NAD/NADH and NADP/NADPH. She outlines the roles of each, and highlights some of the challenges involved in developing assays that can accurately measure these metabolites. She discusses key considerations for successful NAD(P)/NAD(P)H assays and provides examples of how to use these assays to measure either total (both oxidized and reduced) forms of NAD and NADP, or to measure oxidized and reduced forms individually in a single assay plate.

NAD(P)H-Glo™ Assay Mechanism
NAD(P)H-Glo™ Assay Mechanism

Continue reading “Measuring Changing Metabolism in Cancer Cells”

Promega Biotech Ibérica Earns Recognition for Contributions to the COVID-19 Pandemic Response in Spain

Posted on by Promega

Small- and medium-sized companies are critical to the Spanish economy. During 2020 the COVID-19 pandemic made business difficult for many of these companies, yet they have demonstrated strength and resourcefulness and have led the pandemic recovery in Spain in many ways. Recently, Promega Biotech Ibérica was recognized with a Madrid Community SME (small- and medium-sized business) Award along with 15 other companies. The awards were presented by Manuel Giménez, Minister of Economy, Employment and Competitiveness of the Madrid Region, Andres Navarro delegate director of La Razón, and Francisco Marhuenda, director of La Razón. As part of the award, Promega Biotech Ibérica General Manager, Gijs Jochems, was interviewed about the award and Promega’s work in the region.

Gijs Jochems, General Manager of Promega Biotech Ibérica accepts the Madrid Community SME Award.
Gijs Jochems, General Manager of Promega Biotech Ibérica accepts the Madrid Community SME Award.

According to Gijs Jochems, General Manager of Promega Biotech Ibérica, while Promega Corporation is an American multinational company, it remains privately held, which offers a great deal of flexibility to the subsidiaries to adapt to local needs. It also allows the company to place increased emphasis on employee well-being (critical during the pandemic), reinvest profits in research and development, and work to mitigate the impact of company activities on the environment. All these business practices reflect a long-term vision of sustainable business growth.

Continue reading “Promega Biotech Ibérica Earns Recognition for Contributions to the COVID-19 Pandemic Response in Spain”

Meet the Mighty Masked Masters of Measurement

Posted on by Michele Arduengo

Scientific investigation is an iterative process, for which reproducibility is key. Reproducibility, in turn, requires accuracy and precision—particularly in measurement. The unsung superheroes of accuracy and precision in the research lab are the members of your local Metrology Department. According to Promega Senior Metrologist, Keela Sniadach, it’s good when the metrology department remains unsung and behind the scenes because that means everything is working properly.

Holy Pipettes, Scientists! We have a metrology department?! Wait…what’s metrology again?

Callibration technician checks out a multipipettor

Metrology (the scientific study of measurement) got its start in France, when it was proposed that an international length standard be based on a natural source. It was from this start that the International System of Units (SI), the modern metric system of measurement, was born.

Metrology even has its own day: May 20, which is the anniversary of the day that the International Bureau of Weights and Measures (BIPM) was created by the Meter Convention in Paris in 1875. The job of BIPM is to ensure worldwide standards of measurement.

For life scientists, metrology centers around making sure the equipment used everyday—from pipettes to heating blocks to centrifuges—is calibrated and measuring correctly.

Continue reading “Meet the Mighty Masked Masters of Measurement”

Deep in the Jungle Something Is Happening: DNA Sequencing

Posted on by Promega

This blog was written by guest blogger and 2018 Promega Social Media Intern Logan Godfrey.

Only 30 years ago, the polymerase chain reaction (PCR) was used for the first time, allowing the exponential amplification of a specific DNA segment. A small amount of DNA could now be replicated until there was enough of it to study accurately, even allowing sequencing of the amplified DNA. This was a massive breakthrough that produced immediate effects in the fields of forensics and life science research. Since these technologies were first introduced however, the molecular biology research laboratory has been the sole domain of PCR and DNA sequencing.

While an amazing revolution, application of a technology such as DNA sequencing is limited by the size and cost of DNA sequencers, which in turn restricts accessibility. However, recent breakthroughs are allowing DNA sequencing to take place in jungles, the arctic, and even space—giving science the opportunity to reach further, faster than ever before. 

Gideon Erkenswick begins extractions on fecal samples collected from wild tamarins in 2017. Location: The GreenLab, Inkaterra.

Gideon Erkenswick begins extractions on fecal samples collected from wild tamarins in 2017. Location: The GreenLab, Inkaterra. Photo credit: Field Projects International.

The newfound accessibility of DNA sequencing means a marriage between fields of science that were previously largely unacquainted. The disciplines of genomics and wildlife biology/ecology have largely progressed independently. Wildlife biology is practiced in the field through observations and macro-level assessments, and genomics, largely, has developed in a lab setting. Leading the charge in the convergence of wildlife biology and genomics is Field Projects International. 

Continue reading “Deep in the Jungle Something Is Happening: DNA Sequencing”

Just in Time for Wisconsin’s Invasive Species Month: Goats

Posted on by Michele Arduengo
Invasive kudzu vine
Invasive kudzu vine covering a forest

“In Georgia, the legend says
That you must close your windows
At night to keep it out of the house
The glass is tinged with green, even so
As tendrils crawl over the fields…”
—James Dickey (1)

I grew up in Georgia, where on a hot, humid summer day you could almost hear the hiss of growing vegetation, especially the Kudzu as it climbed over fence posts and encroached upon the roadside, the king of invasive species. In Florida you worry about the alligators along the roadside if you have a flat tire; in Georgia, beware the Kudzu.

Invasive species, animal and plant, are an issue in all ecosytems. Imported from distant (and not-so-distant) areas both by accident and misguided intent, invasive species are species that have escaped the checks and balances of natural competitors and predators that existed in their native habitats. This lack of predation and competition enables them to outcompete and overrun other species.

Kudzu may be one of the most recognized invasive species in the United States, but it’s probably not the worst. The zebra mussel is an aquatic animal that has invaded our waterways in Wisconsin. Oak savannahs and prairie ecosystems in the Midwest United States are threatened by many invasive plant species like garlic mustard and blister parsnip. The USDA maintains an extensive invasive species list so.

Continue reading “Just in Time for Wisconsin’s Invasive Species Month: Goats”

Biotech Manufacturing: A Good Machinist is Critical for Your Laboratory Reagents

Posted on by Karen Burkhartzmeyer
Travis Beyer, Machinist Technician, at the CNC milling machine in the Promega machine shop.
Travis Beyer, Machinist Technician, at the CNC milling machine in the Promega machine shop.

It can be easy to forget that Promega is a manufacturing business. Hidden within the well-designed walls of the company’s cGMP Feynman Center, as well as in other facilities on the Madison campus, technicians operate hundreds of machines that manufacture, dispense and package Promega reagents day in and day out. Keeping those high-tech machines running at peak performance is critical, requiring immense skill, precision and even artistry. That’s where Promega Machinist Technician Travis Beyer comes in.

“I get to make stuff,” says Travis who is not afraid to show his enthusiasm for his craft while describing the best part of his job. “There’s a product at the end of the day. Plus I get to support science, and make things that support people’s lives. That’s cool.”

I get to make stuff. There’s a product at the end of the day. Plus I get to support science, and make things that support people’s lives. That’s cool.

The da Vinci Center, another artfully designed building on the Madison campus, houses the Promega machine shop where Travis does his work designing or improving on parts for newer manufacturing equipment or reverse engineering broken or worn parts no longer available for older equipment that still serves its purpose. He makes every machine part imaginable from drive shafts to sensor brackets to filling forks, and his work is critical to manufacturing businesses like Promega, where a downed piece of equipment can cause costly production delays.

An example of a machine part that Travis designs or reverse engineers and then builds to keep Promega manufacturing moving smoothly.
An example of a machine part that Travis designs or reverse engineers and then builds to keep Promega manufacturing moving smoothly.

As he explains, not many manufacturing companies the size of Promega have a fully capable machine shop. They usually send out their work, meaning longer lead times and more expense. But, as its distinctive architecture suggests, Promega is not like many other companies.

Continue reading “Biotech Manufacturing: A Good Machinist is Critical for Your Laboratory Reagents”