‘Netting’ bacteria with DNA: strategies of a social amoeba

Life has survived for more than three billion years because it is robust, and almost no mutations can easily outwit the defense mechanisms built up through eons of exposure to potential pathogens.
–Lawrence M. Krauss

Every second, every minute of your life, your body is under attack. This may be strange to think about, but millions of bacteria, as well as myriad other parasites, are attempting at this very moment to invade the sanctum of your body. Do not be offended, these creatures do not do this out of any sense of malice. They are simply driven by the two greatest necessities of life – survival and reproduction.

Dictyostelium Aggregation
Dictyostelium discoideum

Ever since the first cells arose in the hot, steamy, soup that was our earth’s oceans billions of years ago, organisms have competed fiercely for the same limited resources. Some cells devised ways to halt the growth of or outright kill other cells, while others entered complex beneficial (mutualistic) or harmful (parasitic) interactions with each other. With time, two kinds of life forms emerged – parasites, who attack other organisms to their own benefit and the other’s loss, and hosts, who suffer from the parasites’ attack. A much larger class is that of pathogens – any organism that can directly cause disease in a host is called a pathogen. Host defense mechanisms have, therefore, evolved over eons to outsmart parasites and pathogens. Plants have specialized signaling systems to fight invading bacteria, and multicellular animals like human beings have an immune system with several tiers of defense to combat infection. Yet, at the same time, the parasites have been evolving too, devising sneakier and subtler ways of evading the host’s defense pathways to gain entry and live undetected. Life can, in fact, be described as a continuous arms race between hosts and their parasites, where neither gains the upper hand on the other, even after centuries of creating sophisticated arsenals for the purpose.

This continuous struggle has given rise to some truly ingenious forms of biological innovation. A recent study from Xuezhi Zhang and colleagues, working in a collaboration between the University of Geneva, Switzerland, and Baylor College of Medicine, USA, sheds light on a remarkable and evolutionarily ancient line of defense employed by a class of social amoeba. Simply put, the defense consists of casting a net formed of DNA molecules over bacteria and killing them slowly with poisons embedded in the net.

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Ancient DNA: A story writ in genes

The Dinosaur Debacle

Picture a day millions of years past, in a land as yet untouched by the vagaries of man.

jurassic park photoDense forests stretch in every direction from where you stand, and the air you breathe is hot and humid. Now watch, as a magnificent beast, several feet tall, thunders through the undergrowth in determined pursuit of its prey. Years later, men stumbling upon its bones would name it a dinosaur. The little mouse-like creature it is chasing disappears into a burrow, but not before its mate is snatched up in the dinosaur’s crushing jaws. While the predator stands enjoying its meal, it barely notices the little spot of irritation on its shoulder, where a resourceful mosquito sits feasting on the giant’s blood. As the dinosaur moves on, the mosquito flies off to a nearby pine tree, where it rests for a moment before its next meal. Yet this rest would prove to be fatal, as a drop of the tree’s resin, oozing out from a wound in the tree bark, engulfs the hapless mosquito. The resin solidifies, and over millions and millions of years, turns slowly into amber. In the present day, fossil-hunters discover the piece of amber with the perfectly preserved mosquito inside. It would have been dismissed as a curiosity, if it weren’t for some scientists, who, while examining the fossil, discover a drop of dinosaur blood stuck in the mosquito’s tiny stomach. From this drop of blood, they extract DNA, the molecular blueprint of life. Using this DNA, they are able to build a dinosaur genome artificially, and then clone and produce living dinosaurs, enough to fill an island. Enough, in fact, to form a dinosaur theme park. And thus is a story born, that of Stephen Spielberg’s masterpiece and one of the most iconic films of the 20th century – Jurassic Park.

Mosquito in amber
Mosquito in amber by Oregon State University

Spielberg’s movie, which is based on a book by Michael Crichton, is founded on some very real scientific outpourings of that era. In the 1990s, a number of research groups from around the world reported the extraction of intact DNA from ancient insect fossils preserved in amber. While, to the best of my knowledge, no drop of dinosaur blood with dinosaur DNA was ever recovered from an amber fossil, there were enough and widespread studies of fossilized insect DNA sequences that suggested that this was possible. Yet, in the back of many scientific minds, there was a glimmer of doubt, perhaps fanned by the astounding success rates of such studies. Ancient DNA is notoriously difficult to obtain and analyze, and yet reports of doing exactly so continued to pour in in spades. In 1997, Jeremy Austin and colleagues, of the Natural History Museum, London, decided to try and see whether these studies could be replicated.

Amber Insect Fossil

They took more samples than all the other studies before this had had combined, and used a large number of extraction and amplification methods to try and obtain authentic ancient insect DNA. The results were surprising. Most of the samples did not yield sufficient amount of analyzable DNA, and those that did so were inevitably found to be contaminated with modern DNA. This and other studies later went on to establish that it is virtually impossible to retrieve usable DNA from amberized fossil remains, and all of the sensational reports that had come earlier had failed the key test of scientific validity – reproducibility.

In my opinion, this little story demonstrates everything that is exciting and problematic in the field of ancient DNA research, a field that hit its 30th year in 2014.

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