Mendelspod Podcast

Plant biology too is benefiting from single cell resolution.
Unlike animals, plants cannot move away from environmental stress. They have evolved tremendous biological complexity to stay rooted in one place. Their genomes are complex too, with repeated genome duplications producing families of related genes that can take on different functions. And within a single leaf are many specialized cell types, from photosynthetic and epidermal cells to vasculature and rare trichomes, each with its own patterns of gene expression.
It’s early days for plant science. The field is only beginning to assemble the large, high quality single cell atlases needed to understand that complexity and eventually make better predictions and enable a new world of plant engineering.
Robin Buell and Anita Giabardo join us from the University of Georgia to discuss one of those new atlases. Their BioPoplar project aims to engineer fast growing poplar trees to produce new biomaterials, bioproducts and biofuels. Using Illumina’s PIPseq, Anita and colleagues created an atlas of more than 159,000 cells across the developing poplar shoot.
That resolution matters. The researchers were able to find rare trichome cells, the tiny hairs on leaves whose specialized metabolism makes them attractive little factories for engineered products. They then identified a promoter that can specifically direct gene expression to those cells.
Robin has watched plant genomics progress from Northern blots to bulk RNA sequencing and now to single cell. She predicts that within ten years single cell could become the standard. The ability to see biology cell by cell is not only changing what scientists can discover about plants. It will mostly likely change what they can build.


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What new insights can we learn about cancer when researchers are able to look at the genome and the methylome together?
Recently, Illumina launched its 5-base for Cancer Research Grant Contest to explore that question. Today, the three winners join us on Mendelspod with three very different problems in cancer research.
Richard Tothill of the University of Melbourne is studying cancers of unknown primary and in collaboration with Hartwig Medical Foundation is combining DNA methylation and mutation profiling to reveal the primary origins of these aggressive cancers. Jacob Blum of Johns Hopkins is working with tiny amounts of circulating tumor DNA, combining genetic variants with methylation signals in hopes of improving detection of minimal residual disease and developing a model that other researchers could use. And Alfonso Bellacosa of Fox Chase Cancer Center is investigating what methylation can reveal about the mechanisms behind response and resistance to cancer immunotherapy.
The projects are early stage, but together they give us a snapshot of how cancer researchers are using a new tool that brings epigenetics and genetics into the same experiment and analysis. Joining the discussion is Danielle Goldberg from Illumina, who talks about what the company saw across nearly 200 grant applications and the growing interest in combining genomic and methylation data in cancer research.


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A recent New York Times article highlighted a remarkable study showing that exercise can help keep colon cancer in remission. After eight years, 90 percent of patients in a structured exercise program were still alive, compared with 83 percent in the control group. Yet despite these results, such programs are rarely covered by insurance. It’s a striking example of something our guest today, Mayo Clinic physiologist Mike Joyner, has argued for years. Are we overlooking some of the most powerful ways to improve human health in our pursuit of molecular medicine?
Over a decade ago, we invited Joyner on as a skeptic of the emerging precision medicine revolution. He questioned whether breaking biology into ever smaller molecular pieces would deliver the improvements in human health being promised. Ten years later, we begin by asking Mike a simple question. Was he right? “I think I was more right than wrong,” he says. Despite important successes in oncology and drug development, he argues that precision medicine has yet to make the broad impact on public health its advocates envisioned.
Joyner remains as provocative as ever. He argues that biomedical researchers have become too dependent on engineered animal models and should pay more attention to nature’s own experiments. The discovery of GLP-1 drugs is a case in point. He welcomes their enormous potential for improving public health but worries that people taking them without exercising may lose valuable muscle mass and miss the additional benefits of physical activity.
We also venture into the contentious debate over transgender athletes in women’s sports. Drawing on physiological research, Joyner argues that suppressing testosterone does not fully eliminate the athletic advantages associated with male puberty. For him, the evidence supports maintaining biological sex categories to preserve fair competition for women.
Throughout the conversation, Joyner challenges us to think beyond the molecular and ask a bigger question. Are we doing the kind of science that will actually make people healthier?

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Is biology headed back into the genome?
While much of biology has been expanding outward into single cells, spatial biology and ever more biological context, Žiga Avsec and his team at Google DeepMind are making the case that there is still an enormous amount to learn by going deeper into DNA itself.
Their new AlphaGenome Atlas uses AlphaGenome to predict the molecular effects of every possible single letter change in the human genome. That’s some nine billion variants. Now researchers can easily explore how a variant might affect gene expression, or splicing, or other layers of gene regulation across different cell types. The Atlas also introduces a variant impact score (AVI) designed to help researchers quickly identify which variants deserve a closer look.
Avsec argues that the scale itself opens new possibilities. Researchers can use the Atlas to prioritize rare variants across enormous cohorts, but they can also work backward from the predictions to investigate something more fundamental, the regulatory grammar of the genome. The grammar of the genome—long a provocative idea, but still not cracked. Short DNA motifs could act something like words, and AlphaGenome may help reveal how those words work together to activate or repress genes across different biological contexts.
There are important limitations. AlphaGenome predicts molecular consequences rather than phenotype, and Avsec says the distance between genotype and phenotype remains long and complex. The model also has more difficulty with regulatory elements that far from genes—a proximity issue—and has so far been trained largely on bulk tissue data rather than the much richer universe of individual cell types and cell states.
For now, Avsec just wants researchers to use the Atlas. The portal is free for noncommercial research, and he explicitly invites scientists to tell the DeepMind team what works and what does not. That feedback matters because the Atlas is not being presented as a finished map. It is part of a cycle in which better models suggest better experiments, those experiments generate better data, and better data produce the next generation of models. Bioinformaticians always want two things. Better data and more data.
This may be an argument for where genomics is headed. Rather than AI replacing experiments, Avsec hopes it will give researchers greater confidence about which experiments are worth doing and ultimately lead to more experiments with more positive findings.
The AlphaGenome Atlas is available free for noncommercial research here:
https://deepmind.google/science/alphagenome/

Mass spectrometry has been one of the most powerful technologies in clinical testing for decades. So why is it still largely confined to specialty labs?
Don Mason has spent more than 25 years in clinical mass spectrometry. Now Senior Marketing Manager for Mass Spectrometry at Roche Diagnostics, he says the technology’s strength has also been its weakness: “Part of its power and part of its challenges are linked.” Mass spec is extraordinarily sensitive, selective and flexible, but traditionally requires specialized operators, complicated workflows and batch processing.
That may finally be changing. Last year Roche launched their new cobas Mass Spec solution designed to automate the process from sample preparation through result reporting. It also brings random-access mass spectrometry into the routine clinical lab. Mason says a sample can now produce a numerical result in as little as 34 minutes, compared with turnaround times that can stretch into days with traditional workflows. He points to transplant drug monitoring and antibiotic and antifungal monitoring in critically ill patients as examples where that difference could matter clinically.
But automation isn’t simply about replacing expertise. Mason argues that moving established assays onto standardized systems could free mass spectrometrists to develop the next generation of tests: “This in turn becomes the innovation engine for tomorrow’s routine mass spectrometry-based tests.”
Roche currently has seven assays available in the U.S., with more expected beginning in 2027. Looking further ahead, Mason sees a much bigger transition. Just as MALDI-TOF transformed microbial identification, he predicts LC-MS will become standard equipment in more and more clinical laboratories over the coming decade.


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