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Seminar Reihe

06.12.2017, 04:00 p.m., Lecture Hall 6C

Dunite as sole source of H2 for growth of hydrogenotrophic methanogens

Dr. Anna Neubeck

Astrobiology Centre, University Stockholm, Sweden

30.10.2017, 11:00 a.m.,

Does Metabolism Recapitulate Biogenesis?

Prof. Dr. Joseph Moran

Laboratory of Chemical Catalysis, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), University of Strasbourg, France

05.10.2017, 02:30 p.m., Lecture Hall 6F

On the Origin of Ubiquinone

Prof. Dr. Mauro Degli Esposti

Centre for Genomic Sciences, UNAM, Cuernavaca, Morelos, Mexico and Italian Institute of Technology, Genoa, Italy

30.05.2017, 04:00 p.m., Lecture Hall 6F

The Energy Expansions of Evolution

Dr. Olivia P. Judson

FU Berlin (Institute of Biology), Imperial College London (Department of Life Sciences) and University of Glasgow (Institute of Biodiversity, Animal Health and Comparative Medicine)

The history of the life–Earth system can be divided into five ‘energetic’ epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the trans- formation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life–planet systems elsewhere.


11.04.2017, 03:00 p.m., Lecture Hall 6F

Probing Mineral Surface-Biomolecule Interactions Using Computational Chemistry Methods: Insights of Prebiotic Chemistry Relevance

Prof. H. Chris Greenwell

Department of Earth Sciences, Durham University, United Kingdom

Since the early work of Bernal, among others, mineral surfaces have long been invoked as having a role to play in the origin of life on Earth [1]. In more recent years, mineral surfaces have been shown to be able to concentrate simple precursors to biomolecules from dilute solution, to be able to act as catalytic sites, to template simple biomolecules for polymerisation, and to protect more complex biomolecules formed from degradation [2]. Certain mineral surfaces are also inherently chiral and, recently, redox reactions at mineral surfaces have also become increasingly explored [2].

Despite their utility in facilitating a wide range of biological-like interactions and catalysis in a prebiotic world, processes at mineral surfaces, especially the internal surface of layered minerals, are inherently challenging to study. As a result computer simulation has become an essential tool for studying mineral-biomolecule interactions, giving insight into the structure, dynamics and reactivity of biomolecules at mineral interfaces. Computer simulation is also a powerful tool for testing potential early Earth scenarios and undertaking thought experiments [3].

This presentation will illustrate results from computer simulations of layered silicate and hydroxide minerals with both amino acid/proteins and nucleic acids conducted over the last 10 years.

[1] Bernal JD (1949) The physical basis of life. Proc Phys Soc B 62:752.

[2] Hazen RM and Sverjensky DA (2010) Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb Perspect Biol 2:a002162.

[3] Coveney PV, Swadling JB, Wattis JAD and Greenwell HC (2012) Theory, modelling and simulation in origins of life studies. Chem Soc Rev 41:5430–5446.


03.04.2017, 04:00 p.m., Lecture Hall 6F

Phylogenetic rooting using minimal ancestor deviation

Dr. Giddy Landan

Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts-Universität zu Kiel

Phylogenetic tree reconstruction methods produce unrooted trees, which require an additional analysis – rooting – in order to determine the ancestor-descendant relations of the studied entities. Given its pivotal role for evolutionary studies, it is notable that no major advance in the methodology of rooting has been presented since the publication of Outgroup rooting and Midpoint rooting approaches in the 1970’s. We introduce the Minimal Ancestor Deviation (MAD) rooting method, which operates on any phylogenetic tree with branch lengths. MAD explicitly quantifies the major confounding factor - rate variation among lineages - to achieve unprecedented accuracy and consistency. We anticipate that many long-standing evolutionary controversies will be settled (or at least sharpened) with high-quality rooting.


01.12.2016, 03:00 p.m., Lecture Hall 6A

Why chloroplasts and mitochondria retain their own genomes and genetic systems: Co-location for Redox Regulation of gene expression

Prof. Dr. John F. Allen

Research Department of Genetics, Evolution and Environment, University College London

Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control—control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Co-location of gene and gene product for Redox Regulation of gene expression (CoRR) is an hypothesis in agreement with the results of a variety of experiments designed to test it and that seem to have no other satisfactory explanation. I present evidence relating to the CoRR hypothesis, and consider mechanisms of redox regulation in chloroplasts. I discuss the development, conclusions, and implications of the CoRR hypothesis, and identify predictions concerning the results of experiments that may yet prove it to be incorrect.

Allen JF (2015) Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. Proc Natl Acad Sci USA 112:10231–10238.


Mini Symposium | 30.11.2016, 02:00 c.t., Lecture Hall 5D

Diversity of mitochondria

Prof. Dr. Aloysius G. M. Tielens

Dept. Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, The Netherlands

Dept. Biochemistry and Cell Biology, Utrecht University, The Netherlands

Biochemistry textbooks still depict mitochondria as oxygen-dependent powerhouses of the cell, but many mitochondria can produce ATP without using any oxygen. In fact, several other types of mitochondria exist and they occur in highly diverse groups of eukaryotes – protists as well as metazoans and possess an often overlooked diversity of pathways to deal with the electrons resulting from substrate oxidations. Several types of mitochondrial related organelles (MROs) can be distinguished: aerobic and anaerobic mitochondria, hydrogenosomes and mitosomes. A functional classification and short description of the various classes among the mitochondrial family of MROs will be discussed (with a maybe surprising overrepresentation of parasitic organisms?).

The role of ‘mitochondria’ and ROS in early eukaryotic evolution

Dr. Dave Speijer

Medical Biochemistry, Academic Medical Center, University of Amsterdam, The Netherlands

Reactive oxygen species (ROS) formation by mitochondria is an important eukaryotic process. I will introduce a kinetic model in which the ratio between electrons entering the respiratory chain via FADH2 or NADH (the F/N ratio) regulates ROS formation. I speculate that this mechanism explains peroxisome evolution. I will also link it to the absence of fatty acid oxidation in long-lived cells (such as neurons) and to other universal eukaryotic adaptations, such as dynamic supercomplex formation, carnitine shuttles, uncoupling proteins, and multiple antioxidant mechanisms, especially linked to fatty acid oxidation. Recent findings in the field of peroxisome evolution and peroxisome mitochondrion relationships, ROS formation by Complex I during ischaemia/reperfusion injury, and supercomplex composition adjustment to changes in F/N ratios strongly support the model. I will further discuss the possibility that other eukaryotic inventions (e.g. meiotic sex) can be understood in the light of internal ROS formation by the endosymbiont as well.

Mitochondria, ageing and separate sexes

Prof. Dr. John F. Allen

Research Department of Genetics, Evolution and Environment, University College London, United Kingdom

There is no greater mystery in the whole world, as it seems to me, than the existence of the sexes, – more especially since the discovery of Parthenogenesis. The origination of the sexes seems beyond all speculation."

Charles Darwin: Letter to J. S. Henslow,16 July 1860 [1]

Mitochondria are small organs – "organelles" – that convert energy within the living cells of all animals and plants.  Mitochondria contain chemical reactions that release energy by combining the building-blocks of food with oxygen from the air.  Mitochondria are descendants of bacteria.  Those bacteria were partners in a symbiosis that made the first eukaryotic cells. From their bacterial ancestors, mitochondria now retain complete genetic systems – DNA, RNA, ribosomes – to produce only thirteen of the many hundreds of proteins they need for energy conversion. In cell evolution, why have any genes at all been retained within mitochondria? I outline possible answers, and identify the one I favour [2]. Mitochondria are maternally inherited and carry their few essential genes within an energy-converting, chemically reactive, mutagenic, dangerous, cellular sub-compartment. The action of the energy-converting chemistry on their DNA may explain why our tissues and organs degenerate as we age.  If this is the case, then why is the acquired damage not inherited with the mitochondria that are passed directly, through the egg cell, from a mother to her offspring? Why are babies not born with their mothers' accumulated signs of ageing? A possible answer to this question [3] prompted experiments with surprising results [4–6] and broad implications. Almost all species of animals and plants now appear as individuals that are either male or female, or sometimes both. I propose that sex provides two distinct and complementary vehicles, male and female, to reconcile energy conversion with faithful transmission of mitochondria, with their tiny genomes, between successive generations. Does this theory solve the mystery described by Darwin in his letter to Henslow?

[1] Darwin Correspondence Database. Available from: http://www.darwinproject.ac.uk/entry-2869

[2] Allen JF (2015) Why chloroplasts and mitochondria retain their own genomes and genetic systems: colocation for redox regulation of gene expression. Proc Natl Acad Sci USA 112:10231–10238.

[3] Allen JF (1996) Separate sexes and the mitochondrial theory of ageing. J Theor Biol 180:135–140.

[4] de Paula WBM, Lucas CH, Agip A-NA, Vizcay-Barrena G, Allen JF (2013) Energy, ageing, fidelity and sex. Oocyte mitochondrial DNA as a protected genetic template. Phil Trans R Soc Lond Ser B Biol Sci 368:20120267.

[5] de Paula WBM, Agip A-NA, Missirlis F, Ashworth R, Vizcay-Barrena G, Lucas CH, Allen JF (2013) Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function. Genome Biol Evol 5:1969–1977.

[6] Allen JF, de Paula WBM (2013) Mitochondrial genome function and maternal inheritance. Biochem Soc Trans 41:1298–1304.


14.11.2016, 10:30 a.m., room

Life and times of Hydra

Prof. Dr. Damjan Franjevic

Department of Zoology, Department of Evolution, University of Zagreb

Named after the nine-headed sea snake of Greek Mythology Hydra is a genus of small, freshwater animals found in streams, ponds, and lakes in temperate and tropical regions, that belong to phylum Cnidaria, class Hydrozoa.

Although Hydras are fairly simple animals in terms of their body construction composed of only two cell layers, which are maintained by three independent stem cell lineages they have enormous research potential and appeal due to their simplicity of composition and structure, remarkable power of regeneration and its accessibility to a variety of experimental manipulations.

Interestingly enough Hydra has been used as an experimental organism for nearly three centuries culminating in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. In that light newest discoveries regarding life, “death”, phylogeny and symbiosis in Hydra will be presented alongside the question what’s next to discover in biology using this simple but powerful experimental organism.