COVID


Paul Freemont on Synthetic Biology in the UK

To begin the year, we head across the pond for an outlook on the thriving community of synthetic biology in the United Kingdom.

Paul Freemont was a co-author of the UK's synthetic biology roadmap and co-directs SynbiCITE, the national center for the commercialization of synthetic biology. A few years ago the government put an initial investment of $300 million pounds into the field, and "everything was going swimmingly well," says Paul. "Then COVID happened."

Paul himself was running what is called the London Biofoundry which is similar to what we call an accelerator here in the States--except that it's funded publicly.

"And the pandemic was such a moment because in the UK in March of 2020, we had a total capacity--nationwide-- to do about 10,000 SARS Cov-2 tests. All the hospitals and others didn't have any capacity for testing. So we pivoted our whole Biofoundry to do an open testing platform. Within eight weeks, we had a working platform that was doing 2,500 tests per day."

We know the rest of the story--the UK became a success model for testing during the pandemic. With things stabilizing around COVID and researchers free to go back to business as usual, what excites Paul about synbio today?

He says that scaling for all synbio companies holds some exciting challenges and opportunities right now. As for the 800-pound gorilla we often discuss here in the U.S.--that is PR--Paul says that the UK is a bit of a different animal. Society there is "tech literate" and with the cost of energy skyrocketing this winter, the average person has become much more open, by necessity, to arguments that synbio holds big promise to bring sustainability to a plundered planet.

Mara Aspinall on COVID

Winter is here.  In America, we're just back from the Thanksgiving holiday when many of us travel and get together.  And so far there is no great COVID surge this year. 

Or is there?

Today's guest says there likely is, and we don't know it because of the most significant shift in our pandemic response: at-home testing.  

We're pleased to welcome Mara Aspinall to the program today to update us on the state of COVID.  It's been over a year since we covered the topic, and we're curious about what's going on out there and overall what has been the impact of the pandemic on the diagnostics and genomics fields.  Mara is the co-author of Sensitive and Specific, The Testing Newsletter.   She co-founded the Biomedical Diagnostics program at Arizona State University’s College of Health Solutions and has been CEO of some major diagnostics companies in our space, including Genzyme and Ventana.  She currently advises the Rockefeller Foundation on COVID.

It's coming up on three years since the first Wuhan variant came to our shores in early 2020, and with that hindsight we can now make some interesting observations.  For example, how does it compare to the flu overall?  Mara says early comparisons were way off the mark, but today, the death rate is similar.  Why has the Omicron variant stuck around so long?  And how are we set for the next pandemic?  It's all in here as we catch up on the "state of COVID."
 

Going Beyond Time Barriers: Arutha Kulasinghe on the Power of New Spatial Biology Tools

Arutha Kulasinghe was pumped for the AGBT (Advances in Genome Biology and Technology) Conference this year. He is the Principal Investigator for the Clinical-oMx Lab at the University of Queensland. Dr. Kulasinghe has pioneered spatial transcriptomics using digital spatial profiling approaches in the Asia-Pacific region, contributing to world-first studies for lung, head, and neck cancer and COVID-19. Not gathering last year due to the pandemic, the AGBT conference has became a kind of revival for genome biologists. This year saw an explosion in spatial programming and presentations.

“I almost thought the conference needed to be rebranded as Spatial AGBT.”

Arutha is part of a new generation of biologists who have come of age with spatial tools as part of their biology tool kit. He joins us today to share his experience at the AGBT conference and give his take on the latest in the spatial arena.

The interview takes us into three areas today: the impact of the new tools on pure discovery, Arutha’s COVID paper out last March, and the excitement around the ability of spatial tools to look at old samples.

In the COVID study, Arutha’s group identified a biomarker that was predictive of severe disease. His group is already commercializing the assay with a biotech company. This is a stunning timeline, going from pure discovery to commercialization so quickly, and could only happen with spatial tools.

“It shows you how you’re able to go from discovery using tissue-based approaches to validation of those markers in a peripheral sample, and then develop a blood assay for that,” says Arutha.

The ability of the new tools to look at historical FFPE tissue samples is opening up a new world for researchers. Arutha talks today of a study looking at Spanish flu samples from a century ago and also of not needing to create new cohorts because samples are already there.

We finish up with a look ahead into where Arutha thinks the field is going. He sees H&E stains getting down to the single pixel resolution.

Building on the Knowledge Base of Developer Community, LuminexPLORE Lab Offers Custom Insights: Jackie Surls, Director

There are some technologies that become so ubiquitous in biomedical research that their name turns synonymous with their use. This has been the case for the Luminex xMAP platform and multiple biomarker analysis. The product has been applied in just about every area of life sciences including infectious disease, STD, organ transplant rejection, vaccine development, cancer research, immunodeficiency, animal testing, agriculture, and others. (xMAP is a research use only product and not for use in diagnostic procedures.)

To help this extended community benefit from a broad swath of assay development knowledge, Luminex has set up what they’re calling LumineXPLORE Lab, offering custom assay development. Today, director Jackie Surls takes us on a podcast journey through the lab and shares insight into the many applications of this enduring technology.

DNA Script Takes DNA Synthesis Back to the Bench with Enzymatic Tech: Thomas Ybert, CEO

DNA is a multibillion-dollar industry in 2021 and satisfies many life science applications, including drugs, reagents, siRNA, PCR, diagnostics, synthetic biology, and many others. Enzymatic DNA synthesis, or EDS, is a new approach to manufacturing DNA that is much more efficient and user-friendly and could disrupt the current market.

Thomas Ybert is the CEO of DNA Script which is out with a new benchtop enzymatic DNA synthesizer called SYNTAX. He says in contrast to old chemical synthesizers, the new “DNA printer” takes virtually no expertise to run and will return much of the current business from service back to the old model where biologists make their own, having the power to “go from design to results in less than 24 hours.”

“[Biologists] are programming biological systems. DNA is the programming code. And you want this design-build-test cycle to go as fast as possible. It’s very clear that the next revolution will be from the life sciences. And we want to enable people to design-build-test super quickly.”

Investors appear happy with the company, just pouring in $165 million last month. The SYNTAX system is available now. With all that hassle of chemical synthesis cleared away by this new easy-to-use technology, will researchers and others return to making their own DNA?

A New Way to Phenotype Life: Chris Mason Talks Spatial Biology, His New Book

Chris Mason, Professor of Physiology and Biophysics and prolific genomics researcher at Weill Cornell Medicine, joins us to talk about what he’s doing with the new generation of spatial biology tools.

The first papers we dive into are his work on COVID. Chris says the spatial tools have shown us the ravages of the coronavirus on the body like nothing we’ve seen before, i.e. the tissue damage from the cytokine storms and “the long term perturbations such as seeing cells far apart that were usually hanging out together.”

Does this new resolution open up all kinds of questions for not just the SARS-CoV-2 virus, but for other viruses Chris has long studied? And does he think the pandemic will spark an “age of virology” research?

Chris says he’s using the new spatial tools in his work with NASA as well as his grander metagenomics projects and believes the companies making these new tools are "just getting started."

Speaking of space, Chris has a new book out this summer into which he has poured much of his vast knowledge of genomics and science, his hope for our species, and a personal plea. It’s called, The Next 500 Years: Engineering Life to Reach New Worlds.  Go check it out.

And check out our sponsor links as well. Thanks to NanoString for underwriting this new series.



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