Stanford scientists sequence genome of human's closest invertebrate relative

ORIGINAL: Stanford
By Bjorn Carey 

August 14, 2013

Botryllus schlosseri, a small sea creature, can regenerate its entire body from its blood vessels alone. Stanford researchers hope that sequencing its genome will lead to advances in regenerative and transplant medicine for humans.

Botryllus schlosseri is humans' closest living invertebrate relative. Chris Patton

At first glance, Botryllus schlosseri has very little in common with humans. The small sea creature fuses together with others to form colonies that look like psychedelic blobs, encrusting rocks and seaweeds. It can reproduce asexually, and an entire individual can be regenerated from its blood vessels alone.

And yet, Botryllus is humans' closest living invertebrate relative. (Invertebrates lack a spinal column.) Now, a group led by Stanford scientists has sequenced its genome, making it possible to find the genetic basis for some of the animal's amazing regenerative abilities and immunity features, which potentially could be applied to human medicine.

In total, the group sequenced the animal's 580 million base pairs of DNA. (The human genome, by comparison, consists of more than 3 billion base pairs.) Though the researchers haven't studied the entire genome, they found evidence that Botryllus makes a useful invertebrate model for studying human genetics, in particular for highlighting the evolution of immunity and stem cell-mediated regeneration.

The researchers compared the Botryllus genome with several vertebrate and invertebrate genomes. Focusing on genes involved in various human diseases – affecting things such as heart and eye development, pregnancy and cancer – they found homologous genes for each in Botryllus, far more matches than in any of a dozen other invertebrates commonly used in research.

An additional investigation of blood-related genes revealed that Botryllus was probably the first invertebrate to have vasculature in the same context of the human circulatory system, with blood cells traveling through blood vessels.

For example, in looking at a set of 20 genes that encode for humans' hematopoietic stem cells – cells that can self-renew and differentiate into other types of blood cells – they found 14 that are also expressed in cells isolated from the Botryllus stem cell niche. The scientists are now investigating how these genes function in Botryllus.

"The whole body can regenerate from the vasculature alone: the heart, digestive system, sophisticated tissues," said Ayelet Voskoboynik, a scientist at Stanford's Stem Cell Institute and Hopkins Marine Station, and the lead author on the study. "And it can do this relatively fast, probably using stem cells. Now that we have the genome, we can try to understand the mechanism behind it."

The study of Botryllus' genome could also lead to advances in transplant medicine. When two genetically distinct Botryllus colonies come into contact with each other, they either fuse their blood vessels to create a single organism, or reject one another and maintain individuality. When the blood vessels between the two colonies fuse into one interconnected network, the stem cells from each partner colony begin to circulate throughout the other.

The stem cells compete and in many cases one partner's stem cells "win" – and any new or replacement tissue grown through the fused colony does so based on the "winner's" genetic code.

A similar process occurs in humans who undergo an allogeneic transplant – when a patient receives tissue or cells from a non-identical donor. For instance, if a patient receives bone marrow or a ligament graft from a donor, over time, the recipient's cells replace the donor tissue.

In some instances, particularly concerning transplants of bone marrow or hematopoietic stem cells, the recipient's body rejects the donor cells. Voskoboynik suspects that studying the genetic basis for this interaction in Botryllus could lead to improvements in human therapies.

"If we can learn what makes a highly competitive stem cell a winner, and why others are rejected, we could hope to apply that knowledge to improve the success rate of allogeneic transplantations in humans," Voskoboynik said.

An important byproduct of the research, Voskoboynik said, was that Botryllus' complicated genome required the team to develop a new sequencing technique. The method, which has been patented, yielded exceptionally long, accurate sequences of DNA.

Additionally, rather than creating an average of the genetic information encoded on each paired chromosome, as standard techniques do, the new method yielded individual results from each chromosome. That advance, Voskoboynik said, could play a critical role in studying human diseases that occur as the result of different versions of genes existing on paired chromosomes.

The study was recently published in the peer-reviewed journal eLIFE.

Media Contact
Ayelet Voskoboynik: (831) 655-6244, ayeletv@stanford.edu

Bjorn Carey, Stanford News Service: (650) 725-1944, bccarey@stanford.edu

Pyura chilensis: the closest thing to getting blood from a stone

ORIGEN: Scientific American
By Becky Crew

June 21, 2012

Credit: Arvid Puschnig

“Period Rock? You’re calling me Period Rock now? Guys, seriously, I might look like a stone, but that doesn’t mean I have the heart of one. Why doesn’t anyone ever just call me Michael?”

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Despite appearances, this is not some kind of cruelly bisected alien stone organism or a tomato thunderegg. This is Pyura chilensis, a sea creature that lives on the rocky coast of Chile and Peru. And if (like me, very recently) you’ve never seen one of these before, you’ll probably be interested to know that in Chile, they are fished commercially, and the locals eat them raw or cooked with salad and rice because apparently they’re delicious.

P. chilensis belongs to the Ascidiacea class of non-moving, sac-like marine invertebrate filter feeders that are otherwise known as sea squirts. They belong to the Tunicata subphylum, so-called because they wear thick ‘tunics’ made of tunicin, which is a hardy matrix of molecules that help the animal attach itself to a hard surface on which it will carry out its days. The insides of this tunic are lined with an epidermis and a muscular band, and inside these layers lies the main part of the animal.

P. chilensis has two siphons that connect the animal to the surrounding ocean through its tunicin – one for exhaling and one for inhaling. It eats by inhaling the water and filtering out the edible microalgae using a moving layer of mucus in its enlarged pharynx, or branchial sac, before exhaling the water back out the other siphon. The pharynx is connected to the animal’s digestive tract, which basically acts like a mouth.

Their blood is clear and, strangely, can accumulte extremely high qualities of a mysterious and rare element called vanadium. The concentration of vanadium in the blood of P. chilensis and other tunicates can be up to 10 million times that of the surrounding seawater. Just why and how these creatures are able to accumulate vanadium in such huge quantities remains unknown. 

A Pyura chilensis dish from a market in Valparaiso in Chile

P. chilensis can often be found in densely packed aggregations of thousands or small handfuls of just a few, or they can be found on their own – in which case they must reproduce on their own, as there is no way of them moving to find a mate. This means P. chilensis is hermaphroditic, with the gonads of both a male and a female that can release eggs and sperm simulataneouly to meet as a fertile cloud in the surrounding water. If the sperm-egg collisions are successful, they will produce tiny tadpole-like offspring that will eventually settle onto a rock to grow into the adult form.

In 2005, biologists Patricio H. Manríquez from the Universidad Austral de Chile and Juan Carlos Castilla from the Pontificia Universidad Católica de Chile published a paper in the Marine Ecology Progress Series revealing for the first time the particulars of this creature’s reproductive habits (They also use the verb ‘selfing’ often and with glorious earnestness). They collected 30 sexually mature P. chilensis from habits in central and northern Chile and set them up in lab tanks as isolated and paired individuals. They wanted to assess the occurrence and success of fertilisation via these two types of reproduction followed by the settlement of the resulting offspring to a hard surface and their subsequent metamorphosis into adulthood.

First, the isolated individuals were placed in plastic bottles, and were left alone for 90 days, free to do all the selfing they wanted (YOLO). After this period, their body size relative to the amount of sperm in the water was measured for each spawning episode. Next, the researchers combined pairs either from the same population, or from two different populations, to see how well they would breed in comparison to the selfers. A third experiment saw them keep P. chilensis individuals in isolation for one to 16 months, to see if an extended period alone would improve the success of selfing. Finally, the researchers conducted ‘manipulated ferilisation’, which involved removing eggs from the specimens and fertilising them with extracted sperm in Petri dishes.

The results showed that P. chilensis is born male, before becoming cosexual – having both male and female gonads – in its adolescence as it increased in size. The researchers also found that given the choice – that is, if situated around other individuals – these organisms prefer to breed via cross-fertilisation, writing, “Given that more events of natural egg spawning followed by successful settlement and metamorphosis were recorded in our paired specimens and in our manipulated cross trials … it appears that cross-fertilisation predominates in this species.”

Manríquez and Castilla also found that a greater number of fertilised eggs resulted from the paired specimens, which suggests that cross-fertilisation, or reproducing with another individual, predominates because it is more effective. This assumption was strengthened by the fact that individuals that had cross-fertilised before being put in isolation took at least two months before successfully producing offspring via selfing. However, they were careful to note that while cross-fertilisation was preferred, selfing did not produce inferior offspring. “No perceptible differences in fertilisation, settlement and metamorphosis success among self and outcross progeny were found,” they reported. This suggests that when stuck alone in the ocean, selfing provides an advantageous opportunity for loner P. chilensis individuals to still pass on their genes.

Here’s a video of a German man knifing some P. chilensis with great aplomb to the tune of a handful of angry YouTube villagers.
About the Author: Becky Crew is a Sydney-based science writer, award-winning blogger and former online editor of COSMOS magazine. She is the author of 'Zombie Tits, Astronaut Fish and Other Weird Animals' (NewSouth Press). Follow on Twitter @BecCrew.