Spain to launch an atlas of all living beings cell by cell

Some of the world’s top scientists met on May 15 in Barcelona to discuss the crazy idea of studying each species of living being, cell by cell, in order to complete an atlas capable of shedding light on the evolution of life on Earth and the origin of human thought and disease. Seemingly over-ambitious, the idea came to Arnau Sebé Pedrós, 37, a biologist from the village of La Fuliola in Lleida, in Catalonia, Spain. Sebé Pedrós studies cells, but his real passion is ornithology. He travels to exotic places and makes a point of catching sight of absolutely all bird species in the region, even if he has to spend a week chasing a nondescript brown bird. This all-encompassing ambition may explain his determination to compile what he has called “the Cellular Atlas of Biodiversity.”

Sebé Pedrós works at the Center for Genomic Regulation, close to Barcelona’s Somorrostro beach, once a district of shantytowns and now home to half a dozen cutting-edge scientific institutes. The biologist’s office is small and simple. Three jellyfish, named Gary, Gerry and Cherry, swim around a circular fish tank. From his desk, the researcher proclaims that his project is no longer a pipe dream. The Gordon and Betty Moore Foundation, established in California by the co-founder of Intel and his wife, has just put up €3.6 million to launch the initiative.

Sebé Pedrós already made global headlines in September. His team analyzed the four known species of placozoans cell by cell — strange creatures shaped like tiny pancakes. They are marine organisms barely a millimeter in size, which diverged from the human group 800 million years ago and consist of 50,000 cells each. The meticulous work of Sebé Pedrós and his colleagues has revealed that these tiny beings, lacking a brain or any other organ, possess something similar to neurons, the cells responsible for thought.

The biologist argues that the Cellular Atlas of Biodiversity would reveal a multitude of nature’s secrets. “We have to be prepared to come across unexpected findings,” he says. “Our study of placozoans was not undertaken with a view to understanding the evolution of neurons and the nervous system. That naturalistic motivation is what I like the most. We are explorers.”

Every living being has a unique DNA, present in each of its cells. In the case of human beings, DNA is like a piano with 20,000 keys, which are the genes. All cells have the same piano, but each of them plays a different tune, which is why some are neurons in the brain and others are part of the muscle or the fat around our middle. According to Sebé Pedrós, a couple of years ago, his group created the first cell-by-cell atlas of the cauliflower coral, an organism that forms reefs in the shallow waters of the Indian and Pacific oceans. The analysis revealed 40 different cell types. One of them, in charge of making the coral cling to the rock, constantly touches a key that triggers the production of an antimicrobial compound, as if it wanted to clean up its surroundings. The study of the coral’s cells brought to light a new substance with antibiotic potential during a global alert about the threat of superbugs resistant to all known drugs. “It was a surprise,” says Sebé Pedrós. “The potential for finding new genes with new functions is very high.”

The May 15 meeting in Barcelona was a success, marking the first time that a scientific alliance of this size has been launched in Spain. It was attended by the leaders of the main international organizations in the field, such as the American biologist Harris Lewin, coordinator of the Earth BioGenome Project, which aims to read the DNA of all species of animals, plants, fungi and protists. Also participating were Stein Aerts, the Belgian bioengineer behind the Fly Cell Atlas, and British researcher Mark Blaxter, who studies 70,000 U.K. species in Darwin’s Tree of Life project. The heads of the Human Cell Atlas, the Israeli scientist Aviv Regev and the German Sarah Teichmann, joined via videoconference.

The €3.6 million from the Moore Foundation will be used to launch “phase 0″ of the project, according to Sebé Pedrós. The biologist and his colleagues will fine-tune the methods for analyzing each species and prepare the infrastructure of the vast database, in collaboration with Irene Papatheodorou of the European Bioinformatics Institute in Hinxton, England. “We want to have a home for the data we will start producing on a large scale already set up,” he says.

“There are a lot of people working on this in the world, but there is a lack of coordination,” adds Sebé Pedrós. “When you want to access the results for a species, it’s absolute chaos. There are no standards of any kind. Nor is there a coordinated effort to see who does what. It’s the Wild West.”

Sebé Pedrós is currently putting the finishing touches to an article on the initiative for a leading scientific journal. “I know of many people who have done many experiments that have not worked out, wasting thousands and thousands of euros, but there is no culture of publishing your methods and explaining what has not worked for you,” Sebé Pedrós. “The next person who tries it is back at square one. We want to open up the field and let no one keep their magic tricks to themselves.”

Phase 0 of the project will investigate eight species that have already been analyzed cell by cell in order to test the protocols. This group will consist of the fruit fly, the worm Caenorhabditis elegans, an annelid (also from the worm group), a plant of the genus Marchantia, an anemone, a fungus, a brown algae, and possibly a sea urchin or a starfish. “We want to study organisms that are difficult to handle, with hard casing, to test six cell-by-cell analysis methods,” says Sebé Pedrós. The usual techniques involve breaking the subject into pieces and obtaining a suspension of single cells using force, sound waves and enzymes. This is followed by examining which keys of the DNA piano each cell plays. “We want to obtain a universal method,” says Sebé Pedrós.

The project will open up a new world for science. “Cell atlases not only tell you about the biology of the organism you are analyzing,” says Sebé Pedrós. “You can also study its interactions with what else is inside its cells.” His team has investigated microalgal blooms in the ocean, linked to giant viruses that hijack cellular machinery. Scientists can analyze what type of cells the invaders are in and how they usurp the piano keys.

Sebé Pedrós is already calculating what phase 1 of the project might look like. “We could start with about 100 species spanning the entire tree of life,” he says. “We will need another €10 to €15 million. Ideally, we would like to sample organisms that are on both sides of major transitions, such as the emergence of multicellular beings and the origin of the nervous system.”

Sebé Pedrós grew up among the steppe birds typical of the drylands of Lleida. He has made expeditions to study bird life in North Africa, Turkey, Thailand, Chile and Israel, with more than 2,000 species observed. He recently saw his first Tengmalm’s owl in Spain. In the eastern jungles of Australia, he encountered the mythical cassowary, a bird measuring up to two meters that has been known to kill humans. In his small office in Barcelona there is no decoration, just a drawing of a tapaculo — a brown bird from Chile — and a postcard with the face of Charles Darwin, the father of the theory of evolution by natural selection. “We are interested in studying the evolution of cell types,” he says. “But first there are a lot of technical questions that are dense and boring, but which we need to solve.”

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