Thursday, 25 October 2012

Jurassic Park Rides Again

The famous scene in Jurassic Park during the extraction of the DNA
Anyone who has seen the first film in the Jurassic Park franchise will remember the scene where a needle was inserted into amber and DNA extracted from the stomach of a single mosquito. The DNA was hundreds of millions of years old, but from it a new race of dinosaurs was created.

DNA is a delicate molecule and will inevitably decay over time, but that does not mean that organic structures cannot be preserved. Yet it is incredibly rare. That is why, 20 years ago, when Mary Schweitzer published a report on what she believed to be preserved red blood cells within the bone marrow of a Tyrannosaurus rex bone, her findings were met with disbelief, even ridicule. In 1997, Schweitzer placed a thin slice of bone from the giant carnivorous reptile under a microscope.

She saw small spheres which were organic in nature. Yet was it possible that red blood cells had survived for 65 million years and retained their structure? The bones of this argument (no pun intended) were put to rest during her PhD when she proved that the structures were indeed fossilized cells which had originated from once living dinosaur cells. She reported also finding preserved collagen fibres, the stringy protein which binds cells in tissues together.

Proteins have a specific structure and shape which, when subjected to unfavourable conditions, such as heat or extremes of pH, will undergo a process called denaturation, whereby they lose their shape and structure and cannot act as proteins any more. Being buried and compressed during fossilization would have been enough to destroy any proteins within the bones, but the findings were still published as collagen molecules preserved inside the marrow.

Dr Mary Schweitzer at work
Since then Schweitzer reported the presence of blood vessels, feather fibres and specialized bone cells, called osteocytes, within dinosaur fossils. Despite her conclusive work on the red blood cells, many palaeontologists have remained sceptical of her findings.

Recently, however, she has published a paper which consists of over five years work using some of the most detailed molecular studies ever performed on a fossil.

One of the major theories she had to contend with was that the so called blood vessels and bone cells were actually biofilms, skins of bacteria which formed around the inside of the cavities left by the structures which existed when the dinosaur was still alive, which retained their shape even after the mineralised bone around them was broken away. To counter this, she collected fresh samples.

One was from Tyrannosaurs rex and was recovered from the Hell Creek formation in Montana and the other from Brachylophosaurus from the Judith River Sediments in Montana. The rocky part of the bones were de-mineralised in order to break them down and release the softer materials inside where the potential proteins and osteocytes lay. The process was repeated using bones from an alligator and an ostrich the reasons for which will become clear later.

Some of the preserved structures from inside
the 65 million year old dinosaur bone
Detailed images from powerful microscopes showed that the structures in the dinosaur remains were the same shape and in the same place within the bone. Schweitzer and her team of researchers went deep into the makeup of the structures, right down to the molecular level.

One antibody will only be able to stick to maybe one or two different proteins. It will be unable to bind with any others and so they can be used to identify proteins in  substance. The researchers looked for the presence of two proteins, actin and tubulin. Their distribution in the alligator and ostrich bones matched the distribution found in the dinosaur bones.

To make the proof indisputable, the soil and bacteria from around the bones was subjected to the same test. There was no trace of either actin or tubulin, showing that the structures could not be biofilms. The next question was whether the structures were osteocytes from a dinosaur. This is where the alligator and ostrich osteocytes come in. Birds are descended from dinosaurs. Therefore the osteocytes in both the ostrich and dinosaur bones should share similar properties.

PHEX is a protein unique to avian osteocytes. It can be identified very easily as only one kind of antibody will bind to it. It will reveal the presence of bird osteocytes and as dinosaurs are their ancestors, they should also have PHEX in their bone cells. The dinosaur and ostrich bones were stained with this chemical marker and both gave a positive result. To prove that PHEX is bird and dinosaur specific, the alligator samples received the same test.

It gave a negative result, proving that the bone cells in the fossil were those of a dinosaur. Incredibly, the PHEX proteins had not denatured, even after 65 million years of compression in the baking rocks of Hell Creek. Using yet another identifying chemical, which jams itself between the base pairs of a DNA molecule and glows when subjected to UV light, Schweitzer revealed the presence of DNA in the fossils.

A useful diagram showing where the preserved structures were found
Although in small quantities, it was a distinct and undeniable molecular signature. While it is a limited amount and the entire sequence will have decayed into short fragments, some of it may still be sequenced. It seems that there was a grain of truth to Jurassic Park after all. What is more, several DNA related proteins were found. These only exist in complex organisms which goes against the biofilm hypothesis.

The final question is how did this prehistoric molecular goldmine survive  through time? While the team have published no definitive answers, they have a number of speculations. The first is that osteocytes lie in the heart of the bone where they would have been safe from the damaging effects of microbes and the environment around it. Secondly, as they are also components which do not divide, they live the same length of time as the organism which they make up.

Their final hypothesis is that, upon death, the iron leaking from red blood cells created complex links between the proteins, DNA and cell membranes, resulting in the incredible level of molecular preservation. Schweitzer's and her team refutes the biofilm theory once and for all.