IGC - Computational Genomics Group

Mini-size me! From free-living to parasite

We tend to think of intracellular parasites as a distorted version of Aesop's fable "The Ant and the Cicada" or like a son in his thirties who still lives in his mother's house - does the minimum necessary and takes everything they have to give. This view stems in part from the extensive gene loss displayed by parasite's genomes. But which genes are lost? In order to answer this question, we built a neutral model of evolution simulating a random loss scenario. Deviations from neutrality identify possible signs of selection. We study the distribution of structural domains in free-living and parasites, as these represent units of protein evolution. Interestingly our preliminary results show a preferential loss of duplicates rather than single copies. We interpret this as maintenance of diversity at the expense of loss in redundancy. In this tale the cicada tends to look more like a minimized version of the ant. It may be that it needs a minimal set of genes/proteins for parasitic lifestyle that does not deviate from free-living. Can this imply a physical endpoint? In this seminar we'll try to address the implications of this and future steps in the search of understanding the mechanisms of genome compaction.

Section for Computational Science, Universiteit van Amsterdam

A Look into Stromatolites

Stromatolites are "living rocks" found in shallow waters. They grow due to the microorganisms that inhabit their surface, onto which they cement layer upon layer of sediment. It is a slow process and may take hundreds of years for a stromatolite to reach the height of your knee. They are weaklings, easily destroyed by all sorts of marine life. But they've come a long way. They've been around since the beginning of life on Earth. And they might just prove that life once existed on Mars.

Stromatolites have been on the Earth virtually since the appearance of the first microbes. They dominated underwater landscapes for much of Earth’s history, leaving behind a rich fossil record, sometimes revealing enormous reefs that were built long before sponge or coral even came into existence. Stromatolite frequency declined as diversity of life exploded and today only a few groups of 'living' stromatolites can still be found growing, almost always in special environments.

Ancient stromatolites are very diverse and more than a thousand taxa have been identified over the last hundred years. This diversity arises from the enormous number of biological, geological and chemical factors which may affect their growth. In the case of the most ancient stromatolites, questions have arisen over the role of biology in their growth. Microfossils are almost never conserved the these specimens and it is often difficult, if not impossible, to prove that the microorganisms were even there, let alone built the structures.

In order to help assess whether a stromatolite is biotic, we have chosen to model the microorganisms that build the most impressive stromatolites: filamentous cyanobacteria. From a model of individual filaments, we attempt to simulate the "birth" of a stromatolite. In further research we will attempt to study the effect of cyanobacteria on shaping laminae and also the interaction between the cyanobacteria and other processes.