For the First Time Ever, Gene Expression Can Be Mapped From Space
The University of Notre Dame is collaborating with NASA and Illumina to monitor forest health using cutting-edge technology. The Global Ecosystem Dynamics Investigation (GEDI) sensor, mounted on the International Space Station, uses lidar to create 3D maps of forests. GEDI's data is combined with genetic sequencing from the University of Notre Dame to understand tree health at an unprecedented level. This collaboration, part of NASA's Applied Earth Observations Innovation Partnership, aims to link genetic data with remote sensing to address large-scale environmental challenges. The project utilizes GEDI's lidar, ECOSTRESS's infrared sensors, and DESIS's color patterns to detect early signs of stress and disease in trees. This innovative approach could transform ecological research and forest management.
La Università di Notre Dame sta collaborando con la NASA e Illumina per monitorare la salute delle foreste utilizzando tecnologie all'avanguardia. Il sensore Global Ecosystem Dynamics Investigation (GEDI), installato sulla Stazione Spaziale Internazionale, utilizza lidar per creare mappe 3D delle foreste. I dati di GEDI sono combinati con il sequenziamento genetico dell'Università di Notre Dame per comprendere la salute degli alberi a un livello senza precedenti. Questa collaborazione, parte dell'Innovation Partnership di NASA sulle Osservazioni Applicate della Terra, mira a collegare i dati genetici con il telerilevamento per affrontare le sfide ambientali su larga scala. Il progetto utilizza il lidar di GEDI, i sensori a infrarossi di ECOSTRESS e i pattern cromatici di DESIS per rilevare segni precoci di stress e malattie negli alberi. Questo approccio innovativo potrebbe trasformare la ricerca ecologica e la gestione forestale.
La Universidad de Notre Dame está colaborando con la NASA e Illumina para monitorear la salud de los bosques utilizando tecnología de vanguardia. El sensor Global Ecosystem Dynamics Investigation (GEDI), montado en la Estación Espacial Internacional, utiliza lidar para crear mapas en 3D de los bosques. Los datos de GEDI se combinan con el secuenciamiento genético de la Universidad de Notre Dame para comprender la salud de los árboles a un nivel sin precedentes. Esta colaboración, parte de la Asociación de Innovación de Observaciones de la Tierra Aplicadas de la NASA, tiene como objetivo vincular datos genéticos con sensores remotos para abordar desafíos ambientales a gran escala. El proyecto utiliza el lidar de GEDI, los sensores infrarrojos de ECOSTRESS y los patrones de color de DESIS para detectar signos tempranos de estrés y enfermedades en los árboles. Este enfoque innovador podría transformar la investigación ecológica y la gestión de bosques.
노틀담 대학교가 NASA 및 Illumina와 협력하여 첨단 기술을 사용하여 산림 건강을 모니터링하고 있습니다. 국제 우주 정거장에 장착된 글로벌 생태계 동역학 조사(GEDI) 센서는 라이다를 사용하여 숲의 3D 지도를 생성합니다. GEDI의 데이터는 노틀담 대학교의 유전자 분석과 결합되어 전례 없는 수준의 나무 건강을 이해하는 데 사용됩니다. 이 협력은 NASA의 적용 지구 관측 혁신 파트너십의 일환으로, 대규모 환경 문제를 해결하기 위해 유전 데이터와 원격 센서를 연결하는 것을 목표로 합니다. 이 프로젝트는 GEDI의 라이다, ECOSTRESS의 적외선 센서 및 DESIS의 색상 패턴을 활용하여 나무의 스트레스와 질병의 초기 징후를 탐지합니다. 이 혁신적인 접근 방식은 생태 연구 및 산림 관리를 혁신할 수 있습니다.
L'Université de Notre Dame collabore avec la NASA et Illumina pour surveiller la santé des forêts en utilisant des technologies de pointe. Le capteur Global Ecosystem Dynamics Investigation (GEDI), monté sur la Station Spatiale Internationale, utilise le lidar pour créer des cartes 3D des forêts. Les données de GEDI sont combinées avec le séquençage génétique de l'Université de Notre Dame pour comprendre la santé des arbres à un niveau sans précédent. Cette collaboration, faisant partie du partenariat d'innovation de la NASA sur les observations terrestres appliquées, vise à relier les données génétiques au télédétection afin de relever les défis environnementaux à grande échelle. Le projet utilise le lidar de GEDI, les capteurs infrarouges d'ECOSTRESS et les motifs colorés de DESIS pour détecter les premiers signes de stress et de maladies chez les arbres. Cette approche innovante pourrait transformer la recherche écologique et la gestion forestière.
Die Universität Notre Dame arbeitet mit der NASA und Illumina zusammen, um die Gesundheit der Wälder mithilfe modernster Technologie zu überwachen. Der Global Ecosystem Dynamics Investigation (GEDI) Sensor, der an der Internationalen Raumstation montiert ist, verwendet Lidar, um 3D-Karten der Wälder zu erstellen. Die Daten von GEDI werden mit der genetischen Sequenzierung der Universität Notre Dame kombiniert, um die Gesundheit der Bäume auf einem noch nie dagewesenen Niveau zu verstehen. Diese Zusammenarbeit ist Teil der Innovationspartnerschaft der NASA für angewandte Erdbeobachtungen und zielt darauf ab, genetische Daten mit Fernerkundungstechniken zu verknüpfen, um große Umweltprobleme zu lösen. Das Projekt nutzt GEDIs Lidar, die Infrarotsensoren von ECOSTRESS und die Farbmustern von DESIS, um frühe Anzeichen von Stress und Krankheiten bei Bäumen zu erkennen. Dieser innovative Ansatz könnte die ökologische Forschung und das Waldmanagement revolutionieren.
- Collaboration with NASA and Illumina enhances research capabilities.
- Utilization of GEDI, ECOSTRESS, and DESIS for comprehensive forest health monitoring.
- Potential to transform ecological research and forest management.
- None.
Insights
This collaboration between NASA, Illumina and the University of Notre Dame represents a significant leap in forest monitoring technology. By combining space-based sensors with genetic sequencing, researchers can now map gene expression across entire forests from orbit. This innovation has several important implications:
- Enhanced early detection of forest health issues, including pest infestations and diseases
- Improved understanding of forest responses to climate change and environmental stressors
- Potential for more targeted and efficient forest management practices
For Illumina (
Investors should note that this type of research collaboration enhances Illumina's reputation and could lead to future partnerships in environmental genomics. However, it's important to recognize that the direct revenue impact is likely minimal in the short term, as this appears to be primarily a research initiative rather than a commercial product launch.
This groundbreaking research represents a significant advancement in environmental monitoring capabilities. The integration of space-based sensors with genetic sequencing data creates a powerful new tool for assessing forest health and biodiversity at unprecedented scales.
Key points to consider:
- The ability to map gene expression from space could revolutionize how we monitor and manage ecosystems, potentially leading to more effective conservation strategies.
- Early detection of forest stressors, such as drought or pest infestations, could allow for more timely and targeted interventions, potentially saving billions in economic losses.
- This technology demonstrates the growing importance of interdisciplinary approaches in solving complex environmental challenges.
While the immediate market impact for Illumina may be , this project positions the company at the forefront of environmental genomics applications. Long-term, this could lead to new product lines or services tailored to ecological research and land management, expanding Illumina's market beyond traditional healthcare applications.
Investors should view this as a strategic investment in future capabilities rather than a near-term revenue driver. The potential for this technology to address critical environmental issues could lead to increased demand for Illumina's sequencing technologies in non-traditional markets.
NORTHAMPTON, MA / ACCESSWIRE / September 25, 2024 / Illumina
The University of Notre Dame is partnering with NASA and Illumina to monitor phenotypic signals for entire forests at once
Originally published on Illumina News Center
As you read this, a white box the size of a refrigerator is hurtling through space at 17,500 miles per hour (28,000 kph), shooting four lasers at the Earth 242 times a second. It's called the Global Ecosystem Dynamics Investigation sensor, or GEDI.
GEDI laser beams travel 250 miles (400 km) down to a forest in Michigan's Upper Peninsula and strike a precisely targeted square of trees just 98 feet (30 m) across. Some wavelengths reflect off the canopy; some penetrate to the branches below; others reach all the way to the ground before bouncing back into space.
This technology is "lidar"-like sonar but using light waves instead of sound waves. In a thousandth of a second, the beams return to GEDI, which compares how much each wavelength was absorbed to build a three-dimensional map of that square, including ground topography, foliage density, and canopy height.
GEDI is one of several instruments mounted on the International Space Station that are taking constant measurements of the world's forests. Another, ECOSTRESS, uses infrared light to read leaf temperature. A third, DESIS, separates visible light into thousands of specific wavelengths to see exactly what color pattern the leaves are reflecting-from which you can infer details about the tree's internal structure.
And at the University of Notre Dame Environmental Research Center in Indiana, Professor Nathan Swenson and his students are cross-referencing all this information with genetic sequencing data from trees. By correlating extremely high-resolution images taken from space with the microscopic gene expression patterns of individual leaves, they are creating a map of the forest's health to a degree never before attempted.
Don't miss the forest for the trees
How did tree ecologists and genetic researchers come to use data from space? Their partnership is quite novel, and to find out how they got there, it helps to consider how their work used to be done.
Traditionally, ecologists have assessed forest health by going into the field and measuring a few key traits in sample trees, like wood density and leaf mass per area. Doing this can tell you a bit about how the tree responds to environmental changes, but it's time consuming and not very scalable to the forest at large. So, over the past decade, Swenson has been looking into a new method: sequencing tree transcriptomes.
While genomics chiefly studies DNA, transcriptomics studies messenger RNA molecules, which convey instructions from the DNA to other parts of the cell. An organism's genome typically doesn't change throughout its life-but its transcriptome represents a dynamic snapshot of all the cellular processes that are active at a particular moment, and this varies depending on the organism's current environment.
Swenson ran an experiment: He subjected seedlings in a greenhouse to different drought conditions, and then performed RNA sequencing to see how their genes were responding. The results, he says, ended up more accurately predicting tree health in the wild "than anything else we typically measure in ecology. It's kind of a quantum leap." Later studies confirmed a pattern: The ways that trees expressed certain genes under drought accurately predicted that species' distribution in the wild under the same conditions. "You can't get this information by measuring something as simple as leaf thickness."
Not too long ago, this approach wasn't feasible. Conventional wisdom held that gene expression in the wild is too variable and sequencing it too expensive. "Through time we've learned that it's totally possible," Swenson says. "We're now at about a third of the cost that I used to pay per sample. These things are now within reach, and scalable for the types of samples that ecologists need."
He was onto something. By going from the bottom up-using sample transcriptomes to predict plant response in the wild-he could, as the saying goes, see the trees. But to see the whole forest, and turn those patterns into actionable data, he'd have to go from the top down...the very top.
How inner space met outer space
In 2019, Everett Hinkley, National Remote Sensing Program manager for the U.S. Forest Service, met with Lawrence Friedl, then-director of the Applied Sciences program at NASA. The two of them saw a need for more open conversation between NASA and the government's land management agencies. How could their organizations work together to address each other's research needs, share data, and promote the integration of Earth observational data products into operational land management decision support?
The answer was the Applied Earth Observations Innovation Partnership (AEOIP), which now comprises representatives from NASA, the Forest Service, the U.S. Geological Survey, and the Bureau of Land Management.
In parallel with this collaboration, NASA's Biological Diversity and Ecological Conservation (BDEC) program began looking for opportunities to work with Illumina, since they believe that any aspect of plant health-susceptibility to disease, tolerance to climatic variation, and so on-comes down to genetic variation.
In 2023 they came upon a perfect fit for a BDEC program grant: a proposal from Nathan Swenson to monitor biodiversity by combining space station sensor readings with transcriptome sequences. AEOIP representative Sabrina Delgado Arias, an employee of Science Systems and Applications Inc. at NASA Goddard Space Flight Center, agreed that it could complement work being done by the U.S. Forest Service to map not just drought stress and wildfire risk, but the spread of invasive pests as well.
The key to linking inner space with outer space, it turns out, is leaf reflectance. The way leaves reflect light is strongly correlated with their chemical structure. So from a high enough vantage point, at a fine enough resolution, you could literally map how genetic expression for an entire forest changes over time. Swenson says, "It's a cool science trick...if you can do it."
Taking vital signs from orbit
The three space station instruments used by the project each fill in one part of the picture. GEDI's lidar, which reveals the forest's structure, can show where trees might be losing branches due to sickness. ECOSTRESS's infrared sensors take the trees' temperature, which correlates with how much water they're retaining and their degree of drought stress. And the color patterns detected by DESIS directly reflect the trees' chemical structure due to transcriptomic variation.
For example: The emerald ash borer beetle lays its eggs beneath tree bark, and when they hatch, the larvae feed on the tree's interior. It's especially harmful in North America and Europe, where ash trees haven't evolved natural defenses against it. The external signs of an infestation are often too subtle for the human eye-but they are revealed in leaf color pattern.
The same principle holds for oak wilt disease, a fungal infection. By the time an oak shows obvious effects, it's too late to save it. But the shortwave infrared spectrum reflected by its leaves can show early warning signs.
This work is among the first ever taken of its kind. NASA is currently building a library of spectral characteristics for every plant species in the world, which can ultimately be compared with the recorded genomic variation of that species for even richer insights.
Jeff "Frenchy" Morisette, manager of the Human Dimensions Program at the Forest Service's Rocky Mountain Research Station and a NASA alum himself, is optimistic about the potential applications his agency could put into practice based on this research. "Genetics is as fine a tool as we have to understand why things are happening at the structural level," he says.
Bringing together the best technology and expertise across the sciences
The information-gathering phase of Swenson's project is well underway. With the help of custom tools, expertise, and materials from Illumina, his team at the University of Notre Dame has transcriptomic data from leaf samples collected on site in Wisconsin and Michigan. They're waiting their turn to download orbital imagery taken from the space station this summer, and they plan to begin building statistical models based on the data this fall.
Linking biological variables to remote sensing information massively expands the scope of their research, and everyone involved through AEOIP is buoyed by the promise it holds for changing the way ecologists work. When it comes to applying these extremely cutting-edge technologies for the sake of improving lives and livelihoods across the world, the possibilities seem endless.
"The problems of today are large scale," Swenson says. "There are very few people working on this type of problem, and it really excited me to not stay within our silo to answer these fundamental questions, but to bring in the best technology available from multiple disciplines."
The GEDI sensor (white box in center), mounted on the International Space Station. Photo by NASA
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