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Gina Hagler

December 15, 2019

Sitting Down to Dinner? Make Room for Satellite Statisticians

If you live in the US, it’s likely you’ll eat a meal that includes food that was inspected by the USDA when you sit down to dinner tonight. Some of the food on your plate may be certified organic. Some may have had its genome sequenced and been tracked from field to market. The involvement of these entities alone makes for a crowded table, but you’ll need to make room for quite a few more.

Those responsible for NASA’s Moderate Resolution Imaging Spectroradiometer (MODIS) instruments aboard the Aqua and Terra satellites will need a place. The statisticians at the USDA’s National Agricultural Statistics Service (NASS) Spatial Analysis Research Section who use the MODIS data from those instruments will also join you. And don’t forget the scientists at NOAA and the National Drought Mitigation Center (NDMC) who work with data generated by the Aqua and Terra satellites. You’ll need a few seats for them, too.

Over the past decades, technology has reached aspects of our lives ranging from communication to medicine, entertainment to manufacturing. It’s of little surprise that tech has reached the food on your table in a big way during this past decade. In addition to the use of whole-genome sequencing (WGS) by the FDA to nip foodborne illness outbreaks in the bud, the FDA and NASA are adding another layer of oversight. Through NASS, they are combining satellite surveillance with statistical analysis to increase crop yields and better serve the interests of agriculture – and by extension, you as the consumer at the dinner table. The information available to farmers and those overseeing food-related government programs is used to increase crop yields and inform crop rotation schedules. It also makes it more likely that you will have a steady source of food for your plate.

Satellite Imagery to the Food on Your Plate

One way that farmers can improve their fortunes is by knowing how much competition they face before they plant a specific crop like potatoes. The USDA makes it possible for farmers and other stakeholders in agriculture, to see what is being grown across the country and in their region. The CropScape – Cropland Data Layer (CDL) data is available at no charge through the use of the CropScape NASS data portal. Those visiting the site can focus on regions and areas of greatest interest to them. Companies that market their products to farmers can also access this data through the portal, providing them with information about what types of products will be in demand during the growing season. Any of these parties can view layers on the map that show the different types of crops.

In addition to the images from MODIS, the information for the layers in the CropScape system comes from agricultural advisors, inspectors, and farmers who upload their data to the system. Because they have worked to identify the crops grown in each field and coders have worked to link the data from those reports to the pixel level on the map, an accurate and timely view of crops across the country is available. Historical data is also available to provide insight into which crops have done well in which regions in prior years.

By using algorithms designed to interpret the red, near-infrared and shortwave infrared of satellites capturing images from the land, the CropScape map can not only differentiate by crop, but also by the stage of crop development. The ability to use this technology to see what is growing successfully and what is not, on a national level, provides farmers with the information they require when deciding what to plant. The bottom line for consumers is a steady supply of produce, either in the form of what was expected in the market, like carrots, or an alternative crop.

For the farmer, this LandSat (Earth-observing) technology, also impacts routine decisions related to harvesting their crops. From the images, it is possible to view a specific area, such as a cranberry bog, to see something as small but significant as the peak harvest time for the cranberries in that bog. The use of this free source translates into valuable, actionable knowledge about when to gather that portion of his crop. It saves guesswork and time, allowing them to plan for the best use of resources related to bringing the crop to market.

Recognizing Drought Before it’s Too Late

Some weather events, like torrential rains or hurricanes, are obviously damaging to crop yields. When one of these hits an area, the effect on crops is immediate. With flooding, seedlings don’t root and more mature crops suffer greatly. The weather and winds from hurricanes do significant damage to crops, silos, and equipment. Accurate forecasts can help farmers delay planting if severe weather is on the way, but once the crops are in and growing, preventive measures can only do so much. 

Severe drought is equally damaging. In severe conditions, crops suffer and yields decline, causing shortages at the market along with higher prices. Unlike rainfall or the atmospheric weather conditions that cause hurricanes, droughts are the result of several factors on the ground in addition to the lack of precipitation. There is another type of drought that is every bit as damaging to crop yields. These “Flash Droughts” can damage crops in a matter of weeks.

Farmers needed a method for detecting flash drought conditions before it was too late to save the crop. NOAA took the lead in the development of the Evaporative Stress Index (ESI). This index gives farmers access to data, at no cost, about the state of moisture in their area. Farmers and other stakeholders can not only view drought information on a national map, but they can also input coordinates and see what the estimates are for conditions in their specific area. The index assesses conditions without precipitation, providing a look at how crops are doing with the irrigation provided by the farmer. For farmers, this information can be used to ensure they have a successful season. For you, it’s a matter of ensuring that the agricultural sector is able to meet consumer needs.

The next time you sit down to dinner, the meal you eat will have been brought to you through the efforts of NASA, NASS, the USDA, NOAA, and the FDA, along with teams of farmers, scientists, analysts, and engineers.

Seeing Stress from Space

What is the Landsat satellite program and why is it important?

National Drought Mitigation Center

USDA Estimation of Crop Production

USDA Ag Data Commons

When Drought Threatens Crops

November 11, 2019

When it Comes to Identifying the Source of Foodborne Illness, The Future is Now

Foodborne illnesses are not only an unpleasant personal experience for millions of Americans each year, they’re a logistical concern for businesses, with the potential to drive and keep people (and their dollars) away for good. As our food supply becomes increasingly global, the ability to accurately and quickly identify the source of any pathogen causing a foodborne illness has become exponentially more difficult. To ensure the safety of what we eat, the Food and Drug Administration (FDA) plans to build upon its early success with digital technology and whole-genome sequencing for its New Era of Smarter Food Safety.

Whole-genome sequencing

At its simplest, a genome is the information a cell needs to create an organism. Since an organism’s genome is as unique as a fingerprint, sequencing that genome is the first step in being able to quickly identify just what is making a person sick. Scientists generate the sequence by gathering samples of a particular food in a sterile environment, mashing it up, and conducting the genome analysis. The result is the fingerprint for that specific entity.

The problem is, having this information on hand at the local level is useful only under very limited circumstances. For instance, it would be enough if a group of people became ill after eating a single meal with food sourced locally, in a single sitting at a single event. With a few calls, it might be possible to identify the food causing the illness and take steps to keep it from being shipped to new locations.

More common is the case in which a number of people with nothing in common at first become ill within days of one another. Making a match between the pathogen causing the illness and the pathogen in each food involved is still fairly straightforward – if everything is sourced locally. But what if some of the food comes from sources across the globe? How are the fingerprints for those foods going to be of use in stopping the spread of the illness to additional locations when there is no way to readily communicate with other localities?

GenomeTrakr

So, to bring whole-genome information into play on a global scale, the FDA created a United States-based open-source distributed network of labs in 2013. The result is GenomeTrakr – the stuff of foodie-sci-fi. It makes whole-genome sequences from foods around the world available globally. Any health agency, anywhere on the network, can upload data from a pathogen causing illness in their locality and receive information about entities that match or closely approximate that sequence. In effect, the power of the digital fingerprinting and related DNA sampling now in use in law enforcement  can be put to work for foodborne illness outbreaks by either making a match or reporting that the match is likely to be found within a certain cluster of “related” genome sequences. This game-changing use of whole-genome sequencing has already helped to halt the spread of global foodborne pathogens several times.

A digital framework

But global genome sequencing is still not all that is needed to safeguard the food supply – and your health. Being able to readily access a whole-genome sequence  can tell you which food is the culprit, but how do you know where the food originated, what path it took from field to plate, and where any additional product is currently located on its journey from field to plate?

The FDA’s remedy to this part of the challenge is to digitize the records kept at each step of a food’s journey through the global system. Rather than filling out a paper form that remains local or creating a paper-based dossier that travels with a food shipment, each step along the way will be documented in a globally accessible, digital format. The result will be a system that complements the GenomeTrakr by making it possible to trace the source of a foodborne pathogen to its point of origin in minutes rather than weeks or months.

Why does it matter? It matters because ready access to the genome, the origin, and the trail it traveled will make it possible to stop the flow of this food through the system: It will keep additional people from becoming ill.

A blueprint

As the first step in the FDA’s Strategic Blueprint for this New Era of Smarter Food Safety, agencies and companies from all parts of the food sector met in October to discuss the logistics of the new approach and offer input.  Considerations ranging from ownership of the data to concerns about data transfer were among the many raised. These issues are not not only vital to the integrity of the data in the system, but will also result in a system we can count on when we sit down to eat.

 

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