The hunt for rainforest’s secret recipes

Wednesday 15 Mar 17
by Iben Julie Schmidt


Thomas Sicheritz-Pontén
DTU Bioinformatics
+45 45 25 24 22

About the rainforest

  • Five per cent of the Earth’s surface is covered by rainforest.

  • Fifty to seventy-five per cent of the world’s total biodiversity is found in the rainforest.

  • Only approximately one per cent of the rainforest’s biodiversity has been properly mapped.

  • Seventy per cent of all anticancer agents identified by the US National Cancer Institute comes from the rainforest.

  • Twenty-five per cent of all substances in the pharmaceutical industry in the West comes from the rainforest.

  • It is estimated that up to 50,000 species disappear every year—whereas only approximately 10,000 new species are identified. This means that a wealth of biodiversity is being lost.
A new research project from DTU will map the genetics of the rainforest’s potent plant compounds, making them available to research and industry.

The temperature is boiling hot. The air humidity is close to the 100 per cent and we are wearing long trousers and big chunky boots to protect us from aggressive mosquitoes and creepy-crawlies as we move through the jungle. We are on the outskirts of the world’s largest expanse of tropical rainforest—the Amazonas.

Despite the presence of huge, hairy, spectacularly coloured spiders and ants the size of matchboxes, we are here to study the plants. For within the mass of interweaving green vegetation there are very likely substances that can treat incurable diseases—substances which the pharmaceutical industry can scarcely dream of.

The local guide leads us through the jungle, stopping at each growth, explaining at length precisely the plant’s unique gastronomic qualities or medical properties. We are in Brazil with a team of researchers from DTU Bioinformatics to initiate an extremely ambitious project—the genome sequencing of the rainforest’s plant life.

“The aim is to utilize all the latest technologies we have at our disposal (next-generation sequencing, proteome, metagenome and metabolomics analysis as well as fluorescence spectroscopy) to explore and preserve the rainforest’s incredible biodiversity and genetic wealth before it’s too late,” explains Professor Thomas Sicheritz-Pontén, who is leading the project.

For the rainforest is undeniably under threat. Every year, the Amazonas is shrinking by about 25,000 square kilometres (an area the size of Jutland) due to deforestation intended to make way for farming land. Unfortunately, the very discovery of the medical applications of the rainforest’s valuable plants, for example, has led to certain plant species being endangered. However, this is where this project is decisively different, says Thomas Sicheritz-Pontén:

“We only need a single leaf or a spoonful of soil for our analyses in order to map which substances the plants produce and how they do it. We will also examine the micro-organisms present, as they contribute to the overall gene pool. You might say we are trying to ‘trick’ the plants into giving up their secret recipes so that we can start producing valuable substances by means of synthetic biology—thereby helping to maintain the forest ecosystem rather than interfering with it.”

Chemical warfare

Professor Birger Lindberg Møller from the University of Copenhagen is an expert in the bioactive natural substances of plants and a member of the team in Brazil. He explains how the many interesting substances produced by the plants form part of an advanced chemical warfare, enabling the plants to defend themselves against attacks from microorganisms and insects, for example.

“At the Center for Synthetic Biology, we are in the process of developing methods to produce complex substances in algae—e.g. using sunlight. The challenge is mapping the biochemical synthesis and developing the system in the algae. But once this has been done, the production process is relatively simple, and our plan with this project is to initiate a production in Brazil which will benefit the country in the form of revenue and jobs—and hopefully provide a viable alternative to deforestation for the purposes of livestock farming,” explains Birger Lindberg Møller.

The plan is to begin mapping the genes of some of the plants which we already know offer a specific medical or biotechnological potential—e.g. plants such as Jaborandi, Açaí, and Jambu (see fact boxes). That said, the project must also identify plants which are currently undiscovered.

"The aim is to utilize all the latest technologies we have at our disposal to explore and preserve the rainforest’s incredible biodiversity and genetic wealth before it’s too late."

“Together with highly skilled Brazilian researchers, we’ve already started to sequence the group of plants called Jaborandi, which are currently under threat due to their medical properties,” explains Associate Professor Bent Petersen from DTU Bioinformatics.

“We would never be able to complete a project such as this without a really great research partner in Brazil, and in fact it was our meeting with Guilherme de Oliveira from Vale Institute of Technology (ITV) in Belém that actually crystallized the whole project in our minds.”

Supercomputer at DTU

It was none other than Guilherme de Oliveira who hosted the event throughout the week the team was in Brazil. Immediately after landing, the team was shown around the ITV campus. The Danish researchers visited the laboratories with plants and sequencing machines for genetic analyses—and the basement—so Peter Løngren, Head of Supercomputing at DTU Bioinformatics, could inspect the department's server capacity.

The Brazilian server is not overly impressive—nor does it need to be. Even though the project will generate huge volumes of data, all the complex calculations will be processed by the Computerome supercomputer at DTU, which will be set up to handle the pan-continental cooperation with the help of cloud technology.

The project is not just about generating large volumes of data, but also about processing and applying these data in a smart way—among other things using artificial intelligence. And this is why a group of bioinformaticians who normally sit behind a computer screen at DTU are now relocating to the jungle.

The goal is to train computers to recognize interesting plants or substances—either based on their appearance or their genetic profile— in order to create an intelligent workflow that makes the almost insurmountable task of sequencing the Amazonas a little more manageable.

Rainforest plants in the medicine cabinet

Jaborandi – Pilocarpus microphyllus

Leaves from the Jaborandi plant are used to extract the substance Pilocarpine, which, among other things, is used to treat the serious eye disease glaucoma. The high demand for this substance has meant that the plant is currently listed as an endangered plant species.

In cooperation with the Section for Plant Biochemistry at the University Copenhagen, a research project at DTU Bioinformatics will now identify the genes involved in the biosynthesis of Pilocarpine with a view to subsequently establishing a photosynthesis-driven production of the substance—e.g. in algae.

Jambu – Acmella oleracea

The rainforest also features exciting new plants, which are used in Brazilian cuisine—e.g. Jambu. The green leaves form part of a traditional Brazilian soup with prawns called Tacacá, and the plant is also used in the making of the Brazilian distilled spirit, Cachaça.

The interesting thing about Jambu is that it is more of a physical experience than an actual taste. Moments after ingestion, the plant produces a strong acidic taste in the mouth. This is accompanied by a strong tingling sensation, and finally heavy saliva production. The active ingredient in the plant is the substance spilanthol.

The local population uses the plant to treat toothache, among other things. However, several new studies indicate that the substance may have antimicrobial and anti-cancerogenic properties and that it can be used in the fight against the Zika virus and malaria mosquitoes. Acmella oleracea is therefore an ideal candidate for further study and analysis.

Açaí – Euterpe oleracea

Açaí berries come from the açaí palm tree, which grows along rivers in the Amazon rainforest. The berries, which are harvested in the wild and in plantations, are an important part of the local population’s diet. However, at the turn of the millennium, the berries were brought to the USA, where they were immediately proclaimed as the new ‘superfood’—reportedly possessing cholesterol-lowering and anti-aging properties due to a high content of antioxidants.

Consequently, açaí became one of the fastest-growing food ingredients ever, and supermarkets are now full of products ranging from ice cream to facial creams advertising their açaí content. It has also been claimed that the açaí berry can reduce the risk of cardiovascular diseases, cancer, Alzheimer’s disease, and many other chronic diseases. However, such claims have not been scientifically documented.

The Brazilian research institution Embrapa (Brazilian Agricultural Research Corporation, Ministry of Agriculture) is conducting research into açaí. The team visited Embrapa and the possibility of a cooperation regarding the gene sequencing of açaí palm is currently being investigated.

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23 MARCH 2017