The thought of an expensive instrument falling out of use and gathering dust on the shelf is enough to bring a tear to any lab manager’s eye. An instrument that once served a key purpose and now functions only as a “paperweight” is a tragic waste of valuable resources. Fortunately, it is sometimes possible to breathe new life into neglected tools and to retrofit or repurpose equipment to meet the new needs that will inevitably arise in a changing lab environment.
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.
It has become increasingly evident to scientists that the intellectual prowess of your average crow has been roundly underestimated. With remarkable skills including superior social acumen, analogical thinking and the ability to craft and use tools, crows seem to prove themselves more and more clever with every investigation into the inner workings of their small, but mighty, brains.
Most recently, new research has revealed that crows may be capable of recursion, a hallmark feature of advanced linguistic ability originally posited by Noam Chomsky in his hierarchy of grammars. Recursion in language is used to grow the complexity of sentence structure to contain, in theory, an infinite number of embedded elements or ideas. Put simply, linguistic recursion refers to the nesting of one grammatical structure, this sentence for example, within another of the same kind. Formerly thought to be a skill exclusive to primates, research like that recently published in Science Advances has challenged this assumption.
Wastewater surveillance, or wastewater-based epidemiology (WBE), is a rapidly growing field that has recently proved effective in tracking the spread of SARS-CoV-2 in communities around the world. WBE refers to the process of analyzing the wastewater output from a population to detect the presence of certain compounds or pathogens. Though its use became widespread during the pandemic, many see its ongoing utility in monitoring other infectious diseases as well, including polio, influenza and monkeypox, among others.
One such application of this tool is taking place at the University of Nevada-Las Vegas (UNLV), where Edwin Oh, Ph.D., is leading a WBE study to keep tabs on disease dynamics in southern Nevada, an area with a population of roughly 2.4 million.
“We do wastewater surveillance for both urban and rural sites, in terms of wastewater treatment plants. We process those samples and we’re able to assess how much virus might be present,” said Oh, who is an associate professor at the Nevada Institute of Personalized Medicine (NIPM) in the UNLV School of Medicine. “We also run wastewater surveillance for specific facilities at the building level, including dormitories, elementary schools and shelters, as well as airports and hotels.”
In late May 2022, Promega invited the nine finalists for the Promega Brazil Young Researcher Award to present their work at a Student Research Symposium on the Promega Madison campus.
The Brazil Young Researcher Award program was created to acknowledge exceptional work by Brazilian students utilizing Promega products in their research. These student researchers were recognized for their achievements and were given the opportunity to present their innovative research to Promega scientists as part of a week-long immersive experience on the Promega campus.
African Swine Fever is a highly contagious disease caused by the African Swine Fever Virus (ASFV) that can spread among populations of both wild and domestic pigs. While not transmissible to humans, it is passed between pigs through direct contact with bodily fluids or feces, through the consumption of contaminated food or through tick-borne transmission. With a mortality rate nearing 100%, this virus can easily devastate large populations of pigs.
ASFV is extremely resilient and is predominantly carried by wild pigs and soft ticks of the Ornithodoros genus. It can survive extended periods of time in processed meat, and contaminated pig products are a common source of transmission, posing a serious threat to the global pig industry due to rising demand for pork. The consequences of unchecked spread of ASFV can include a disruption in the production and exportation of pork products, job losses and other devastating effects. Among those countries with pig populations vulnerable to the spread of ASFV is the Philippines.
Tracking the spread of COVID-19 has been a tremendous challenge throughout the pandemic, but doing so is a key step toward containing the virus. Many communities have relied on patient testing and contact tracing, with limited success. In search of better methods, some countries have made inroads in a different form of disease surveillance: wastewater-based epidemiology (WBE). This approach involves testing wastewater for the presence of pathogens, primarily through DNA and RNA analysis, and has proved to be an accurate and highly effective way to keep tabs on the prevalence and progression of COVID-19 at the population level.
Switzerland is among those countries that have implemented WBE in their efforts to stay ahead of the pandemic. Since WBE first emerged in 2020 as a promising tool, several Swiss laboratories undertook wastewater testing, and protocols were established early.
“At the beginning, the methods to actually detect coronavirus in wastewater were rather laborious and complicated, and involved a lot of resources,” said Dr. Claudia Bagutti, microbiologist and molecular biologist in the State Laboratory of Basel-City, Switzerland.
Bagutti heads a small team performing applied biosafety research. In 2020, her lab was tasked with developing an assay for detecting COVID-19 in wastewater. However, the available methods were prohibitively complex and resource intensive.
In the meantime, researchers at Promega recognized that Promega products and methodologies could potentially be applied to WBE and set to work developing simpler and more efficient method for wastewater analysis. In the spring of 2021, Bagutti’s team decided to try adopting this method.
“Promega had a very nice method which was less laborious and much easier to handle, and that’s why we gave it a try,” said Bagutti.
In the ensuing study, Bagutti and her team analyzed effluent from the catchment area of one municipal wastewater plant in Switzerland. They examined the total wastewater output of around 270,000 people. Viral RNA was extracted using Promega’s Maxwell® RSC Environ Wastewater TNA Kit. The number of RNA copies present, representing the overall concentration of COVID-19 in each sample, was determined via quantitative reverse transcriptase (RT-qPCR) using the GoTaq® Enviro Wastewater SARS-CoV-2 Systems, also from Promega. The viral RNA was subsequently sequenced with next generation sequencing, and the results correlated quite well with the COVID-19 cases in the catchment area. Remarkably, this study detected the Omicron variant in a wastewater sample one day prior to the first reported case identified through patient testing.
“We observed a similar spread to most other western countries with respect to the time of the first discovery of these variants,” said Bagutti. “We were also able to demonstrate the presence [of Omicron] in the wastewater before it came up in a sample of a COVID-19 patient test, which of course shows the usefulness of wastewater monitoring for the prediction of new variants and infection dynamics.”
WBE is especially promising in that it provides population-level data independent of patient testing. Health departments can be alerted to the presence of COVID-19 earlier than would otherwise be possible with traditional testing and can take precautions to contain the spread. In creating a more user-friendly method for wastewater analysis, Promega has opened the door for more laboratories to conduct WBE, which could provide communities around the world with the information they need to preempt the progression of COVID-19.
“The Promega method is very straightforward to handle,” said Bagutti. “It only takes a small volume of wastewater, which makes it handy. It’s less time-consuming compared to the methods which were in the literature at the beginning of the pandemic, and it just works very well. We also did experience great support from Promega.”
At this point, much of the wastewater analysis performed in Switzerland is done with the Promega method, including in federal, state or private labs. The swift advance of WBE in Switzerland speaks to the colossal effort put forth both by Promega researchers in developing the necessary products and methodologies, as well by those labs that have made use of Promega’s products to monitor COVID-19 in wastewater.
“It’s really been a success story for us, from the beginning,” said Bagutti.
Learn more about Promega’s work with wastewater-based epidemiology.
Lynch syndrome, named for American physician Dr. Henry T. Lynch, is a hereditary condition that causes a predisposition to several types of cancer, most commonly colorectal but to other types as well, including ovarian, endometrial and stomach cancer. The root of this disorder lies in a genetic defect known as DNA mismatch repair deficiency (or dMMR), which affects the process by which mistakes are repaired when our DNA is copied during cell division. People with Lynch syndrome can have up to an 80% increased lifetime risk of developing colorectal cancer, and are more susceptible to developing colorectal and other types of cancers at an earlier age. Accounting for 3-5% of all colon cancers, Lynch syndrome is an excellent target for preventative treatment, like a vaccine. Research exploring a Lynch syndrome vaccine seeks to harness the body’s innate immune response to target tumor cells and has yielded promising results.
Automating a workflow can be a tedious and challenging process that requires lots of time and resources. A helping hand can make all the difference, as it did for Stephanie Dormand, Molecular Supervisor at UniPath Women’s Health, a diagnostics lab located in Denver, Colorado.
The women’s health molecular testing service at UniPath primarily relied on the tabletop Maxwell® RSC Instrument to conduct nucleic acid extractions using the Maxwell® Viral TNA Kit. As their testing needs grew, they required more throughput. Dormand worked with Promega Field Support Scientist Rick Grygiel to implement the Maxwell® HT Viral TNA Kit on the Tecan Fluent 780 liquid handler, raising their throughput from 16 to 96 samples per run. When COVID-19 struck, Dormand worked with Rick to quadruple their testing with the addition of another Fluent 780.
Imagine that you’re putting together a large, complex jigsaw puzzle, comprising thousands of exceptionally small pieces. You lay them all out and attempt to make sense of them. It would be far easier to assemble this puzzle were the pieces larger, containing more of the image advertised on the box. The same can be said when sequencing a genome.
Traditional short-read or next-generation sequencing relies on DNA spliced into small fragments (≤300 base pairs) and then amplified. While useful for detecting small genetic variants like single-base changes to the DNA, this type of sequencing can fail to illuminate larger variations (typically over 50 base pairs) in the genome. Long-read sequencing, or third generation sequencing, allows more accurate genome assemblies, facilitating better detection of structural variants like copy number variations, duplications, translocations and inversions that are too large to identify with short-read sequencing. Long-read sequencing has the capability to fill in “dark regions” of a genome that are unfinished and can be used to assemble larger, more complex genomes using longer fragments of DNA, or high-molecular weight (HMW) DNA.
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