Halloween Costumes: Retro Science Style

Your Promega Connections bloggers were sitting around reminiscing the other day, “Back when I was in the lab…”. Kind of like Thanksgiving Dinner among your elderly relatives, it wasn’t long before we were one-upping each other with horror stories from our days at the bench–stories that included escape artist rats, a leaky sequencing gel apparatus, and the iconic radioactively contaminated post doc.

We decided to turn that conversation, with a lot of help from our favorite science cartoonist Ed Himelblau, into retro Halloween costumes based on our memories of things we used to do in the lab that don’t seem like such a great idea now. Enjoy…and if you have a few retro horror science costume ideas of your own you would like to add, feel free to comment.

First up: Cesium Chloride Preps.

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H7N9 Influenza Virus: A Perfect Pathogen?

Artist’s rendition of a virus particle.

It’s late October and here in Wisconsin, like many of you, we are experiencing a change of seasons, with the associated drop in temperatures, changes in leaf color and later this week, Halloween.

Another thing that comes with fall is the start of cold and flu season. By “flu”, I mean influenza, caused by avian influenza viruses of the H-N type. Recent research results by teams at UWI-Madison and in Japan, makes the coming influenza season potentially more scary than usual.

In a recent Cell Host & Microbe paper, M. Imai et al. study a seemingly more virulent version of H7N9 avian influenza virus that is startling in its ability to spread from infected to healthy animal models. Based on a current epidemic of H7N9, human-to-human transmission with this strain is increasing. Continue reading

BioTech Scientists through a Different Lens

When I was in grad school and pictured what a role in industry would look like, the first thing that came to my mind was a Research and Development (R&D) Scientist. My life as a grad student and as a postdoc revolved around benchwork, so that must be the case in industry too, right?

It really wasn’t until I started working at Promega that this image of a scientist in industry was completely turned upside down (in a good way). Here are some roles that a scientist can assume at Promega: Senior Scientist, Research Scientist, R&D Group Leader, Production Scientist, Technical Services Scientist, Product Manager, Strategic Marketing Manager, Client Support Specialist, Client Support Consultant, Clinical Technical Consultant, Field Support Scientist, Applications Scientist, Scientific Instructional Designer. The list can probably go on for a while, but it makes the point that there are a variety of interesting positions for scientists in the biotech industry.
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Coffee and Science–A Cartoon Perspective

Although never actually on the lab bench,  coffee makers have had a prominent place in every laboratory I have worked in. It is because of my laboratory coffee experiences that I am able to drink coffee at any temperature and at any time of the day. The credit for my preference for really strong coffee (with cream, I confess)  goes to two Russian labmates who insisted on making the coffee every morning and went through two bags of beans a week (we had a very wide awake lab).

In all the labs, keeping track of whose turn it was to buy the coffee supplies was just as important as keeping track of whose turn it was to defrost the freezers. I am sorry to say we never thought of a log book because that might have saved me some frantic early morning trips to the store.

Does your lab have coffee rules or traditions? I’d love to hear what they are.

Evaluating DNA Quantity and Quality in FFPE Tumor Samples After Prolonged Storage Using the ProNex® DNA QC Assay

When tumors are surgically removed from cancer patients, the tumor samples are often stored as formalin-fixed and paraffin-embedded (FFPE) tissue blocks. In many cases, tumor samples need to be analyzed several years after diagnosis in order to develop target treatments. But what happens to the DNA after years of storage in FFPE blocks? How well is the DNA preserved?

Scientists in France tried to answer this question in a recent study published in Virchows Arch. The authors extracted DNA from 46 FFPE tumor samples of lung, colon and the urothelial tract, all stored between 4–6 years at room temperature. They then compared the quantity and quality of the DNA to DNA that had been extracted before storage. Using common fluorimetry and qPCR methods, the authors found that the total amount of DNA extracted decreased by half. In addition, the percentage of amplifiable DNA decreased from 56% to only 15% after prolonged storage. Continue reading

Rwanda – Africa’s Next Biotech Hub – Welcomes Promega

Promega sponsored a preconference workshop for grad and undergrad students at the University of Rwanda’s biotechnology campus in Huye, the capital city of Rwanda’s Southern Province.

More than twenty years after the Rwandan genocide when some 800,000 people were killed in just 100 days by ethnic extremists, Rwanda is on a path to not only healing and order, but also technological advancement. Now politically and functionally stable, which is an exception to the rule in east Africa, the country is recognizing that biotechnology is one of the key drivers to help improve the health and well being of its citizens. Rwanda is focusing on providing the resources and training needed to grow its capabilities in biotechnology, and could be on track to become an African biotech hub.

Rwanda, and its biotech push, caught the attention of Promega by way of customers working with its Belgium-Netherlands-Luxembourg (BNL) branch office. Researchers who are also African ex-patriots working at Université libre de Bruxelles (ULB), a French-speaking private research university in Brussels, Belgium, invited Promega to attend a conference in Rwanda earlier this month organized by the Society for the Advancement of Science in Africa (SASA) and the Rwanda Biotechnology Association focusing on translational science and biotechnology advances in Africa. Promega was a main sponsor of the conference along with US medical device manufacturer Medtronic. Continue reading

Tick, Tock! The Molecular Basis of Biological Clocks

A long time ago, before the rise of humans, before the first single celled organisms, before the planet even accumulated atmospheric oxygen, Earth was already turning, creating a 24-hour day-night cycle. It’s no surprise, then, that most living things reflect this cycle in their behavior. Certain plants close their leaves at night, others bloom exclusively at certain times of day. Roosters cock-a-doodle-doo every morning, and I’m drowsy by 9:00 pm every night. These behaviors roughly align with the daylight cycles, but internally they are governed by a set of highly conserved molecular circadian rhythms.

Jeffrey Hall, Michael Rosbash and Michael Young were awarded the 2017 Nobel Prize in Physiology/Medicine for their discoveries relating to molecular circadian rhythms. The official statement from the Nobel Committee reads, “…this year’s Nobel laureates isolated a gene that controls the normal daily biological rhythm. They showed that this gene encodes a protein that accumulates in the cell during the night, and is then degraded during the day. [They exposed] the mechanism governing the self-sustaining clockwork inside the cell.” What, then, does this self-sustaining clockwork look like? And how does it affect our daily lives (1)?

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Biotechnology in Space: Partnering with the Wisconsin Space Grant Consortium

The BioPharmaceutical Technology Center Institute (BTC Institute) has been a member of the Wisconsin Space Grant Consortium (WSGC) since 2002. As an educational arm of NASA, the mission of WSGC “is to use the excitement and vision of space and aerospace science to equip the citizens of Wisconsin with the math, science and technology tools they need to thrive in the 21st century.”

Also as noted on WSGC’s website, “The mission of NASA’s Space Grant Program is to contribute to the nation’s science enterprise by funding education, research, and informal education projects through a national network of university-based Space Grant consortia.” Members of these consortia include academic institutions, government agencies, businesses and other educational organizations, such as the BTC Institute.
Of particular relevance to the WSGC/BTC Institute partnership, Space Grant Program goals include working to:

  • Recruit and train professionals, especially women, and underrepresented minorities, and persons with disabilities, for careers in aerospace related fields.
  • Develop a strong science, mathematics, and technology education base from elementary through university levels.

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Better NGS Size Selection

One of the most critical parts of a Next Generation Sequencing (NGS) workflow is library preparation and nearly all NGS library preparation methods use some type of size-selective purification. This process involves removing unwanted fragment sizes that will interfere with downstream library preparation steps, sequencing or analysis.

Different applications may involve removing undesired enzymes and buffers or removal of nucleotides, primers and adapters for NGS library or PCR sample cleanup. In dual size selection methods, large and small DNA fragments are removed to ensure optimal library sizing prior to final sequencing. In all cases, accurate size selection is key to obtaining optimal downstream performance and NGS sequencing results.

Current methods and chemistries for the purposes listed above have been in use for several years; however, they are utilized at the cost of performance and ease-of-use. Many library preparation methods involve serial purifications which can result in a loss of DNA. Current methods can result in as much as 20-30% loss with each purification step. Ultimately this may necessitate greater starting material, which may not be possible with limited, precious samples, or the incorporation of more PCR cycles which can result in sequencing bias. Sample-to-sample reproducibility is a daily challenge that is also regularly cited as an area for improvement in size-selection.

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Analysis of a biosimilar mAb using Mass Spectrometry

Several pharmaceutical companies have biosimilar versions of therapeutic mAbs in development. Biosimilars can promise significant cost savings for patients, but the unavoidable differences
between the original and thencopycat biologic raise questions regarding product interchangeability. Both innovator mAbs and biosimilars are heterogeneous populations of variants characterized by differences in glycosylation,oxidation, deamidation, glycation, and aggregation state. Their heterogeneity could potentially affect target protein binding through the F´ab domain, receptor binding through the Fc domain, and protein aggregation.

As more biosimilar mAbs gain regulatory approval, having clear framework for a rapid characterization of innovator and biosimilar products to identify clinically relevant differences is important. A recent reference (1) applied a comprehensive mass spectrometry (MS)-based strategy using bottom-up, middle-down, and intact strategies. These data were then integrated with ion mobility mass spectrometry (IM-MS) and collision-induced unfolding (CIU) analyses, as well as data from select biophysical techniques and receptor binding assays to comprehensively evaluate biosimilarity between Remicade and Remsima.

The authors observed that the levels of oxidation, deamidation, and mutation of individual amino acids were remarkably similar. they found different levels of C-terminal truncation, soluble protein aggregates, and glycation that all likely have a limited clinical impact.  Importantly, they identified more than 25 glycoforms for each product and observed glycoform population differences.

Overall the use of mass spectrometry-based analysis provides rapid and robust analytical information vital for biosimilar development. They demonstrated the utility of our multiple-attribute monitoring workflow using the model mAbs Remicade and Remsima and have provided a template for analysis of future mAb biosimilars.

1. Pisupati, K. et. al. (2017) A Multidimensional Analytical Comparison of Remicade and the Biosimilar Remsima. Anal. Chem 89, 38–46.