New Genetic Spectra Across Earth’s Cities & Far Beyond

by Chris Mason, guest contributor

Since speaking at TEDMED 2015, there have been a number of updates to the science I described in my talk. These areas include: space genomics, beer-omics, extreme microbiomes, global city metagenome sampling, epitranscriptome discoveries in RNA viruses, and DNA as music in microgravity.

Image based on images courtesy of ShutterstockSpace Genomics and Genomic DJs

First, we have completed the first whole-genome sequencing profile of two astronauts’ genomes (the Kelly Twins). Also, in collaboration with our NASA collaborators, (Aaron Burton and Sarah Castro-Wallace) we have been sequencing DNA in microgravity; this will be used for 2016 plans to send an Oxford Nanopore Sequencer onto the International Space Station with astronaut Kate Rubin. We are preparing for the return of astronaut Scott Kelly to Earth next week, and are strategizing how to make genome-guided medicine a part of the standard of care for new astronauts. Our goal is to monitor, protect, and potentially repair astronauts’ biology through an integrated view of the layers of the genome, transcriptome, proteome, all the epi-omes, and the microbiome.

In collaboration with Harvard Medical School’s Consortium on Space Genetics, we’ve formally launched a new research focus for Weill Cornell medical students on the study of space genetics and aerospace medicine. This allows new medical students to learn and train in the methods of space genomics, data analysis, and new technology development for space missions. They’re also trained in synthetic biology, materials science, nanofabrication, microbiome engineering, and gene drives. These skills are taught in our class called “How to Grow Almost Anything (HTGAA) – NYC” that is part of the BioAcademany. Work by Elizabeth Hénaff in the 2015 class also helped with our plan for the Gowanus Canal and extreme microbiomes.

Extreme Microbiomes

Microbiomes can lead to a bounty of discovery for new biology, drugs and molecules. We have been systematically hunting for these microbes around the world as part of the eXtreme Microbiome Project (XMP). Among those sampled sites, we have already found that Brooklyn’s Gowanus Canal, a SuperFund site, holds a suite of unique and potentially protective microbes, and we have been designing artificial sponges to hold these in the canal during the remediation process. This is part of a larger project of urban microbiome monitoring and design, called the Brooklyn Bioreactor, which is a collaboration between our laboratory at Weill Cornell, the landscape architecture firm Nelson Byrd Woltz, the Gowanus Conservancy, and the community laboratory Genspace. Lastly, in collaboration with Shawn Levy at HudsonAlpha, we have started collecting data about beer microbiomes, which show an interesting blend of differences depending on the yeast strain used.

Global Metagenome Collection Day

The Metagenomics and MetaDesign of Subways and Urban Biomes Consortium has now reached 43 cities around the world, and a global City Sampling Day (CSD) event is planned for June 21, 2016, to match the collections of the global Ocean Sampling Day (OSD) group. These seasonal molecular snapshots will begin to expand our search for novel microbiomes, new molecules, will aid us in mapping the distribution of antimicrobial resistance (AMR) markers, and enable a better understanding of urban biology and ecosystems.

Epitranscriptome Discoveries and Sounds of RNA

Last but not least, we have just published the first demonstration of another realm of RNA modifications, collectively called the “epitranscriptome.” Specifically, we show that HIV’s RNA genomes also harbor modified RNA bases, and they impact how infectious the virus may be for a patient. We are now on a search across all RNA viruses to see how common these types of modifications are. We are also working to get direct RNA sequencing in nanopores operational, to enable listening to the “music” of the genome as it moves through the pore, as we demonstrated was possible with single enzymes in 2012. These methods and algorithms can help us discern new and peculiar nucleic acids that might be found not only in our lab, but in far-flung places on Earth and beyond.

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In his TEDMED 2015 talk, geneticist and urban metagenome researcher Chris Mason of Weill Cornell Medicine shares how he’s mapping his expertise into the distant future of outer space in the interest of humanity’s interplanetary survival.