The tabletop centrifuge slowly hums to a stop. Tubes are opened and closed, the pipettor moves efficiently into action…it’s just another typical day in the life of a graduate student as you finish setting up your incubation. You decide it’s time for a coffee break! You step out of the lab and fill up your mug in the break area. Sipping away, you begin contemplating your next experiment…as the salty wind sweeps through your hair and the warm Atlantic waves lap at the side of the laboratory.
OK, so this may not be a typical day for a graduate student, unless you’re working in one of the most unique labs in the world – the portable, seafaring “Ship-Seq”.
Science at Sea
Ship-Seq, as the name suggests, is in fact a sequencing and molecular biology laboratory afloat in the ocean. Specifically, it is a high-tech lab retrofitted inside a large steel shipping container that can be moved between different ships, depending on the scientific mission. For University of Florida researcher Dr. Leonid Moroz, the head scientist behind the project, the mission is simple: Sequence some of the most fragile invertebrates of the seas in order to gain a better understanding of animal evolution and to unlock the secrets of regeneration. His organism of choice is the humble ctenophore (pronounced TEEN-oh-fore). Ctenophores are commonly called “comb jellies”, named as such for the iridescent, comb-like rows of cilia lining their bodies and tentacles. These delicate creatures resemble jellyfish, but occupy their own ancient phylum at the base of the tree of life.
Ctenophore species display incredible diversity in body shape and size, and most exhibit remarkable regenerative capabilities. For species living in the pelagic zone (near the surface of the ocean), regeneration is a key adaptation to life in turbulent waters. However, a few species of ctenophores live in deeper, calmer waters, and lack the ability to regenerate. Moroz wants to understand how this difference in regenerative capability plays out at the molecular level, and why some ctenophore species regenerate faster or slower than others. Studying such questions in ctenophore biology and genomics has been nearly impossible in the past, as comb-jellies are difficult to transport intact back to labs on land for experimentation or sequencing. Therefore, to better investigate these organisms in their natural habitat with the highly sophisticated tools of the modern bench scientist, Moroz developed the floating lab concept with colleagues and investors in Florida. Eventually, he found a home for Ship-Seq aboard a retrofitted 141-foot yacht, the Copasetic.
Data on Deck
Aboard the Copasetic, delicate ctenophore samples can be observed and processed as soon as they are removed from the ocean. Lab animals are scooped directly from the ocean and manipulated in various neurobiology and regeneration experiments. Lab equipment and sequencing machines sit atop specially engineered anti-vibration tabletops that move with the waves of the ocean. Sequencing data is beamed back to supercomputers on land via satellite for same-day analysis – a pretty neat set up for the seafaring or landlubber scientist alike. Thus, researchers at sea can sequence RNA and DNA from whole organisms or even single cells as part of a strategy for discovering master regulators of regrowth and healing. Many other species are catalogued to compare genomes or transcriptomes across the ctenophore phylum.
By combining field observations and behavioral and physiological studies with state-of-the-art sequencing technologies, Ship-Seq researchers are bringing the molecular blueprint of the ctenophores’ extraordinary existence to life. Thanks in large part to the work done on Ship-Seq, the ctenophore genome and several transcriptomes have now been sequenced and published (Science 2013, Nature 2014). As such, Moroz’s study of the “aliens of the sea” is beginning to re-write some of the most fundamental rules of animal biology and phylogeny (how organisms are related to each other). We now know that these animals were among the very first kind of multicellular life on earth, and have evolved neural and muscle systems that are analogous to, and yet uniquely divergent from, all other animal lineages. A distinct lack of common developmental pathways, coupled with large expansions of RNA-editing enzymes and glutamate-based neurotransmitters, hints at “new” ways of regulating development and function. And of course, the golden questions remain: How is regeneration accomplished so rapidly among the comb-jellies, and what elements of this ability are conserved, and therefore potentially controllable, in vertebrates? By using Ship-Seq-based approaches to establish ctenophore models of regenerative biology, Moroz and others may ultimately answer these questions and find biomedical applications for those of us who walk on land.
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