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Seminar: Physics of Evolution – Übersicht

  • Übersicht

Which biophysical processes could lead to the first living systems? How can Darwinian evolution be triggered by nonequilibrium processes? Can we build the strategies of life bottom up in the lab? The minimal requirements for the emergence of an evolutionary dynamics are three processes: replication, mutation, and selection. To maintain the genetic simulation, also a nonequilibrium system is needed. We will discuss recent progress in understanding this phase transition from nonliving to living matter. Topics will include experimental and theoretical treatments.

Informationen zur Vorlesung

Zeit und Ort

Fr. 12.15-14.00
H206 Schellingstr. 4 (2nd Floor)

The Seminar is geared towards Masterstudents, however talented, late Bachelorstudents willing to digg deep into more special concepts are also welcome. Papers will focus on recent advances on the topic (not older than say 3 years - exceptions for some classic papers)

Prof. Dieter Braun
(email: dieter.braun@lmu.de)

Papers and Topics (ZIP with PDFs)  Additional_Papers (21-22)

16.10. Introduction and distribution of topics

23.10. Topic 16: The Expanding View of RNA and DNA Function, Highly Efficient Self-Replicating RNA Enzymes ( Julian Nguyen)

30.10. Topic 2: Survivability and reactivity of glycine and alanine in early oceans: effects of meteorite impacts ( Philipp Eulenberg)

6.11. Topic 1: High-energy chemistry of formamide: A unified mechanism of nucleobase formation ( Felix Zeidler)

13.11. Topic 8: Structural motifs in RNA, Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloopA thermodynamic study of unusually stable RNA and DNA hairpins (Florian Hendrich )

20.11. Topic 10: Elements of Metabolic Evolution (Vera Langer)

27.11. T opic 7: Template-Directed Synthesis in 3’- and 5’-Direction with Reversible Termination The strength of the template effect attractingnucleotides to naked DNA (Sebastian Wolff)

4.12. Topic 9: Growth dynamics and the evolution of cooperation in microbial populations ( Oriol Servera Sirés)

11.12. Topic 12: The Origin of Membrane Bioenergetics (Saskia Bruhn)

18.12. Topic 20: Heat flux to replicate and select of oligonucleotides towards increasing length ( Sophia Schaffer)

8.1. Topic 6: Tube Formation in Reverse Silica Gardens. Compositional analysis of copper–silica precipitation tubes (Niklas Köhler)

15.1.Topic 3: Evolutionary games of condensates in coupled birth–death processes (George Dadunashvili)

22.1. Topic 5: Microfluidic Formation of Membrane-Free Aqueous Coacervate. Bioreactor droplets from liposome-stabilized all-aqueous emulsions Droplets in Water (Robert Reichert)

29.1. Topic 11: Experimental generation of volcanic lightning ( Klara Kulenkampff)

5.2. Topic 22:  Noise-Induced Mechanism for Biological Homochirality (Jonathan Liu)

 

1 High-energy chemistry of formamide: A unified mechanism of nucleobase formation
High energy sources - in this case a former high energy laser from Garching - triggers a radical CN und NH chemistry that can form a large number of interesting biomolcules. While the measured mechanisms might not happen often in early Earth (no Lasers ;) the approach sheds some interesting light into radical chemistry for the first metabolisms

2 Survivability and reactivity of glycine and alanine in early oceans: effects of meteorite impacts
Impact is another way to create prebiotic molcules - again this reaction pathway might be less frequent, again we learn about how amino acids are low energy molecules which a generated by overcoming an activation barrier. Also we learn again a lot about how the analysis techniques for Amino acids work.

3 Evolutionary games of condensates in coupled birth–death processes
In a recent theory paper by Erwin Frey, the analysis methods and language of game theory are applied to a wide range of local phase transitions. While perhaps very theoretical, it can lay some groundwork for the following paper on DNA phase transitions.

4 Continuous gelation of DNA in a heat flow
Thermal gradients generated by heat flow can trigger molecule accumulation. The limit of accumulation is merely set by the volume of the molecules. In a manuscript from Christof Mast / Braun group, the local phase transition of DNA is described. The question arises why the phase transition occurs and whether it could be used to implement sequence replication against the degradation of moleucles.

5 Microfluidic Formation of Membrane-Free Aqueous Coacervate
Bioreactor droplets from liposome-stabilized all-aqueous emulsions Droplets in Water
Coacervates are clusters of hydrophobic molecules - in one case with and in another without lipid membrane surroundings. Coacervates are interesting gel-like forms which can mimick cellular functions, also possible platforms for prebiotic reactions which are then half in water and half inside the hydrophobic coacervate. The papers describe recipes to give a clear size and composition definition.

6 Tube Formation in Reverse Silica Gardens
Compositional analysis of copper–silica precipitation tubes
A common non-equilibrium setting is a ion concentration gradient. One case is when the coflow of two species forms a rocky membrane at its interface. The papers describe two cases. Near hydrothermal outflows, similar membranes can form and in topic 12 we discuss connections to the most early proteins in such a setting.

7 Template-Directed Synthesis in 3’- and 5’-Direction with Reversible Termination
The strength of the template effect attractingnucleotides to naked DNA
The Richert Lab in Stuttgart are working to elucidate precise numbers for the affinity of single nucleotides when binding to a single stranded template. Especially the binding to both sides of neighboring bases are important. The ultimate aim is to improve on the prebiotic template-directed synthesis.

8 Structural motifs in RNA
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloop
A thermodynamic study of unusually stable RNA and DNA hairpins
Recently, we got quite interested in Tetraloops, 4-base turning corners of RNA or DNA since they show very interesting catalytic self-ligation activity and might have played a role in the origin of the genetic code. The papers give an overview over different modes of RNA to bind to itself.

9 Growth dynamics and the evolution of cooperation in microbial populations
From the abstract of a recent paper by the Frey group. Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles.

10 Elements of Metabolic Evolution
Behind a grand title is the recent progress along the lines of Günter Wächtershäuser, i.e. the possible prebiotic metabolism to create the first carbon molecules. They explored reductive carbon fixation in a volcanic hydrothermal setting, driven by the chemical potential of quenched volcanic fluids for converting volcanic C1 compounds into organic products by transition-metal catalysts.

11 Experimental generation of volcanic lightning
Don Dingwell et.al. here at LMU are experts in creating synthetic volcanic eruptions. In this paper they demonstrate how to recreate volcanic lightning in the lab. The non-trivial experimental conditions will be explored. Since lightening was used in the past to create interesting first molecules, the approach could be interesting to be used for prebiotic chemistry.

12 The Origin of Membrane Bioenergetics
Bill Martin is one of the experts to trace back the biological tree towards the first elements conserved in the genetic code. The paper gives an overview on how the first biological membrane could consist of based on the genetic evidence.

13 Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea
We look into an important step in later evolution: Archaebacterial halophiles (Haloarchaea) are oxygen-respiring heterotrophs that derive from methanogens—strictly anaerobic, hydrogen-dependent autotrophs. Haloarchaeal genomes are known to have acquired, via lateral gene transfer (LGT), several genes from eubacteria. The paper will illuminate how to reconstruct events in early evolution.

14 Origins of major archaeal clades correspond to gene acquisitions from bacteria
The three branches of biology - archaea, bacteria and eucaryotes - are for the case of archaea traced back. From the protein composition, the later division of archaea is traced back to a gene transfer mechanism. They have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample.

15 Formation of oligopeptides in high yield under simple programmable conditions
Wet-dry-cycles are an efficient way to polymerize peptides (and also RNA). Here an automated approach is used to rapidly explore a number of experimental conditions. The funniest part of the paper is the materials method with the sentence: “Finally, the array of experiments was started by pressing the START button.” - well they removed this sentence from the proof prior to publication.

16 The Expanding View of RNA and DNA Function
Highly Efficient Self-Replicating RNA Enzymes
The papers give a good overview on ribozymes, spanning a wide range and focussing on those with unusual properties. For example, to ligate another ribozyme together for exponential “replication” or to help the addition of unnatural amino acids to tRNA to reprogram the genetic code.

17 Limits of Neutral Drift: Lessons from the In Vitro Evolution of Two Ribozymes
With many years of experience in the molecular evolution of active RNA molecules, Gerald Joyce gives an overview over the mechanisms of evolution found in these experiments: The relative contributions of adaptive selection and neutral drift to observed genetic change are unknown, but likely depend on the inherent abundance of functional genotypes in sequence space and how accessible those genotypes are to one another. To better understand the relative roles of selection and drift in evolution, local fitness landscapes for two different RNA ligase ribozymes were examinedusing a continuous in vitro evolution system under conditions that foster the capacity for neutral drift to mediate genetic change.

18 Flexizymes: Their Evolutionary History and the Origin of Catalytic Function
A Versatile tRNA Aminoacylation Catalyst Based on RNA
Hiroaki Suga from Tokyo is known for a very interesting RNA molecule: one that can reprogram the genetic code by inserting the wrong, unnatural amino acid to a known tRNA molecule. The two papers give a good introduction to the mechanism and history of this interesting appro­ach: ransfer RNA (tRNA) is an essential component of the cell's translation apparatus. These RNA strands contain the anticodon for a given amino acid, and when “charged” with that amino acid are termed aminoacyl-tRNA. Aminoacylation, which occurs exclusively at one of the 3 0 -terminal hydroxyl groups of tRNA, is catalyzed by a family of enzymes called aminoacyl-tRNA synthetases (ARSs). In a primitive translation system, before the advent of sophisticated protein-based enzymes, this chemical event could conceivably have been catalyzed solely by RNA enzymes.

19 Reprogramming the genetic code in vitro
A highly flexible tRNA acylation method for non-natural polypeptide synthesis
Going more into the details, the second series of Suga papers is more focused on the biotechnological details of reprogramming the genetic code: Here we describe a de novo tRNA acylation system, the flexizyme (Fx) system, for the preparation of acyl tRNAs with nearly unlimited selection of amino and hydroxy acids and tRNAs. The combination of the Fx system with an appropriate cell-free translation system allows us to readily perform mRNA-encoded synthesis of proteins and short polypeptides involving multiple non-natural amino acids.

20 Heat flux to replicate and select of oligonucleotides towards increasing length
The replication of nucleic acids is central to the origin of life. On the early Earth, suitable non-equilibrium boundary conditions such as a heat flux across an open pore in submerged rock concentrates replicating oligonucleotides from a constant feeding flow and selects for longer strands. The combined feeding, thermal cycling and positive length selection opens the door for a stable molecular evolution in the long-term microhabitat of heated porous rock.

21 Freeze–thaw cycles as drivers of complex ribozyme assembly
The emergence of an RNA catalyst capable of self-replication is considered a key transition in the origin of life. However, how such replicase ribozymes emerged from the pools of short RNA oligomers arising from prebiotic chemistry and non-enzymatic replication is unclear. Here we show that RNA polymerase ribozymes can assemble from simple catalytic networks of RNA oligomers no longer than 30 nucleotides.

22 Noise-Induced Mechanism for Biological Homochirality
The observed single-handedness of biological amino acids and sugars has long been attributed to autocatalysis. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here, we presenta theory for a stochastic individual-level model of autocatalysis due to early life self-replicators.

BraunEvo1516

Verantwortlich für den Inhalt: Dieter Braun