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THE spring 2019 volume 16 PRIMER issue 2 in this issue 2019 JGI Meeting ..........2-3 NeLLi Symposium Highlights ...4-5 Science Highlights ..........6-7 Save the Dates ..............8 Dimensions of Omics Diversity Study senior author Diane Dickel in her lab. (Thor Swift/Berkeley Lab) Notes from the 2019 JGI Technique for Studying Gene Expression Meeting Takes Root in Plants Natural Selection in Rice Excerpted from the Berkeley Lab release by Aliyah Kovner Kicking off the 14th Annual JGI Genomics of Energy & Environment Lawrence Berkeley National a toehold into its function. In our Meeting in San Francisco, Calif., Laboratory (Berkeley Lab) research- study, we showed that Drop-seq can Michael D. Purugganan, Dean of ers, including scientists at the U.S. help us do this.” Science at New York University, Department of Energy (DOE) Joint Dickel has been using Drop-seq focused on two projects to better Genome Institute (JGI), a DOE Office on animal cells for several years. An understand how selection acts on of Science User Facility, have immediate fan of the platform’s ease the rice genome. successfully used an open-source of use and efficacy, she soon began One project involves developing RNA analysis platform on plant cells speaking to her colleagues working a rice fitness consequence map to for the first time. The technology, on plants about trying to use it on help crop breeders looking for called Drop-seq, allows scientists to plant cells. regions with mutations and pheno- see what genes are being expressed However, some were skeptical that typic variations. It’s based on the and how this relates to the specific such a project would work as easily. INSIGHT (Inference for Natural functions of different cell types. First off, to run plant cells through Selection from Interspersed Genomi- Prior to this study, published in a single-cell RNA-seq analysis, they cally CoHerent elemenTs) method Cell Reports, Drop-seq had only must be protoplasted — meaning developed for human genome been used in animal cells. they must be stripped of their cell studies. The greenINSIGHT method “For many of the genes in plants, walls using unique cocktails of Puruggunan’s lab developed over we have little to no understanding enzymes. Secondly, some plant four years calculates the fitness of what they actually do,” explained biologists have expressed concern impact of mutations that may be senior author Diane Dickel, who that cells are altered too significantly neutral, nearly neutral or advanta- studies mammalian genomics in by protoplasting to provide insight geous. The method allowed the team the Lab’s Biosciences Area. “But into normal functioning. And finally, to identify the rare gene variants and by knowing exactly what cell type or some plant cells are simply too big map them back to the genome. The developmental stage a specific gene to be put through existing single-cell Rice FitCons Map is expected to be is expressed in, we can start getting RNA-seq platforms. available summer 2019. continued on page 7 continued on page 2 THE PRIMER 2019 JGI Meeting continued from page 1 Purugganan also cited the use of study the effects of drought, using uted to microbial infections, and how rice gene expression selection to stable isotope probing to find and these understandings have been measure the contribution of the map pathways of root carbon consum- linked to terms used to describe transcription levels to fitness. This ers into the soil, and using the data illness, starting with the use of is a project he waited more than for network analyses and food web “virulent” to mean “full of poison.” a decade to execute. Partnering with modelling. The team has gone from Twenty years ago, Casadevall began the International Rice Research isotopically labelling grasses in thinking of disease as an outcome Institute in the Philippines, Purugga- greenhouse chambers to field sites at of an interaction between a pathogen nan’s team used samples from plants the Hopland Research and Extension and its host. With that definition, that were either under well-watered Center in northern California. he began trying to find a mathemati- or intermittent drought conditions. “We can’t understand any interac- cal way to track the pathogenic Among their early findings from the tions without recognizing interactions potential of microbes, including fungi. resulting dataset of more than 15,000 among soil inhabitants,” she said. The fungal kingdom, Casadevall genes: they’ve found a “drought- Most interactions studied have been reminded the audience, has more escape” gene that causes the plant in isolation, such as plants and than six million species and includes to flower early. bacteria, or bacteria and viruses, but several pathogens currently doing these studies don’t give researchers significant damage to plants, insects the full picture. “We now have the and whole ecosystems. Humans and tools that enable exploration of the mammals, he noted, are compara- complex interactions that occur in tively resistant to fungal pathogens; soil,” she added, listing an arsenal credit goes to adaptive immunity that includes omics, isotopic tools, and high body temperatures. mass spectroscopy, statistics, All of this led Casadevall back and modelling. to the question of the great lizards: “Don’t ask what killed the dinosaurs, ask ‘What kept the reptiles from having a Second Reptilian Age?’” The answer is the same as the question of why Michael Purugganan humans are here and others he raised at the beginning of his talk: fungi. Fully Understanding Soil Microbiome Interactions In her keynote address, Mary Firestone of the University of California, Berkeley, emphasized the need to Mary Firestone understand the full picture of soil microbiome interactions. The com- plexity was underscored by the plethora of research collaborations, Preventing a Second and lab members past and present Reptilian Age who have helped describe the interac- In his closing keynote, Arturo tions within and across domains thus Casadevall of the Johns Hopkins Arturo Casadevall far to better understand the composi- School of Public Health led with the tion and function of soil microbiomes. human existential questions, “Why Firestone’s long-term goal is to are we here?” and “Why do we eat Diversity in All Dimensions learn about the interactions among so much?” to explain why dinosaurs Geri Richmond, noted chemist plants, bacteria, fungi, viruses and no longer roam the earth. at the University of Oregon and mesofauna in the soil. She talked He briefly recapped how people a strong advocate for diversity in the about work using dominant grasses have come to understand the origins scientific workforce, asked attendees in northern and southern California to of illnesses before they were attrib- to consider serving as a mentor to the 2 / spring 2019 / volume 16 / issue 2 THE PRIMER 2019 JGI Meeting next-generation workforce. “Good innovation and high impact research thrives on diversity in all dimensions,” she reminded them. Richmond should know; alongside her research career, she is founding director of the grass- roots organization COACh, which has helped advance the careers of thou- sands of women scientists and engineers around the world. Among her accolades are the National Medal of Science and the 2018 Priestley Medal, the American Chemical Society’s highest honor. “Social diversity causes discomfort and we have to work harder,” she acknowledged while highlighting the economic benefits of diversity, “but that brings out the creativity.” She asked attendees to consider mentor- ing, serving in the short-term either Annual JGI Meeting Poster Session as a coach who can help refine specific skills, or as a sponsor who can help advance someone’s career, the fungi need LOV — the light, logical implications of automation in or else as a long-term mentor who oxygen & voltage protein domain in biofoundries and multiomics facili- supports and encourages someone’s Neurospora crassa. ties, including the JGI. She pointed growth and development. Aesthetics aside, he added, the out that in the challenge of scaling up images produced through fungal production and reducing human error, “All You Need is LOV” bioluminescence raise several scien- researchers may not recognize that tific questions, including transcrip- they’re shifting their thinking from Some fungi can sense to environ- tional dynamics, cell-cell communica- how to conduct the experiment to how mental factors such as light and tions, and fungal adaptation to light. they can optimize and efficiently use gravity, and respond by changing their Continuing with the photography the equipment. Building a facility and growth patterns accordingly. Luis analogy, Larrondo’s team built a pin- the underlying infrastructure, she Larrondo of the Pontificia Universidad hole camera to allow the “blind” reminded the audience, is about Catolica de Chile combines synthetic Neurospora to sense light intensities. giving the team’s vision and aspira- biology and what he calls “optogenet- They did this by developing a promot- tions form, and making design ics,” how cellular processes can be er that responds to light, and then choices that reflect this goal. activities or repressed by light and combining it with Neurospora’s Frow asked attendees to consider genetics, to learn more the circadian circadian clock that controls daily the relationships between machines rhythms in fungi. rhythms in gene expression. The and humans, adding that while the Larrondo demonstrated how fungi result: an image that slowly appears human component isn’t often taken streaked on a plate can distinguish and then fades over the course of into account when developing work- light intensities. The image is a day, and then reappears following flows, somehow the information and projected onto a plate on which the the fungal cycle. skills need to be transferred. “Infra- fungi are growing. The plate acts as structure for bioengineering requires a photographic film, and after the Worldbuilding with the complex integration of mechani- fungi have genetically processed the cal, digital, biological and human light, they emit bioluminescence in Automation systems,” she concluded.

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