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Subway Seminar on Darwinian DNA Machines (LMU/TUM) – Übersicht

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Dozenten:

Dozenten

Informationen zur Vorlesung

Zeit und Ort

N110 Altbau Physik (Seminarraum Kotthaus/Rädler) an der LMU

Seminarinhalt

Wir werden Paper diskutieren, die zwischen DNA Maschinen und der molekularen Evolution vermitteln.

Zeit: Mittwochs, 17.15 - 19.15;
Vorbesprechung: 22.10.

Ort: Seminaraum N110, Altbau der Sektion Physik:
Seminarraum Lehrstuhl Kotthaus/Rädler an der LMU downtown.

Alle Paper als Zip-File (28MB)

1__22.10. Overview and introduction to the topic (Braun/Simmel)

Selection of the seminars and presentation skills.

2__29.10. In vitro selection: SELEX (Simmel)

* Paper: (Christoph Wienken, Dieter)
Joyce: Forty years of in vitro evolution (2007)
Szostak: In vitro selection of functional nucleic acids (1999)

3__5.11. Continuous in vitro evolution (Braun)

* Paper: (Christof Mast, Dieter)
Joyce, Continuous in vitro evolution (1997)
Joyce, Promise and Perils of continuous in vitro evolution (2005)

4__12.11. Compartimentalized and microfluidic in vitro evolution (Braun)

* Paper: (Ralf Jungmann (?), Fritz)
Tawfik, Compartmentalization (1999)
Griffith, Directed evolution (...) by in vitro compartmentalization (2003)
Griffith, In vitro evolution in microfluidic systems (2004)
Joyce, Darwinian Evolution on a Chip (2008)

5__19.11. The error threshold: the Eigen model of replicating molecules (Braun)

Paper:
Introduction: http://en.wikipedia.org/wiki/Error_threshold_(evolution)
Eigen: Selforganization of Matter and the Evolution of Biological Macromolecules (1971)
Biebricher & Eigen: The error threshold (2004)

6__26.11. DNA Display. Constructing the Library. (Simmel)

Paper:
Halpin: DNA Display I-III. Sequence-Encoded Routing ... (2004)

7__3.12. The historical roots: The Qbeta replicase experiments (Braun)

* Paper:
Spiegelman: The synthesis of self-propagating (...) (1965)
Spiegelman: An extracellular darwinian experiment with a self-duplicating nucleic acid molecule (1965)

8__10.12. Ecoli evolution in microfluidics (Simmel)

Paper: (Simmel)
Keymer-Austin: Bacterial metapopulations in nanofabricated landscapes (2006)

9__17.12. Basic Principles of Replicators and “Elongators” (Braun)

* Paper: (Mario Herzog, Dieter)
Szathmary: A Stochastic Model of Nonenzymatic Nucleic Acid Replication: ‘‘Elongators’’ Sequester Replicators /2007)
Szathmary: The origin of replicators and reproducers (2006)

10__7.1. Entropic driving of DNA machines (Simmel)

* Paper: (Günter Kugler, Fritz)
Zhang: Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA (2007)
Seesaw: A simple DNA gate motif for synthesizing large-scale circuits (2008)

11__14.1. Theory of evolution and subexponential growth (Braun)

* Paper: (Philipp Reineck, Dieter)
Szathmary: Adaptive Dynamics of Parabolic Replicators (2001)
Szathmary: Survival of Replicators with Parabolic Growth Tendency and Exponential Decay (2001)
Szathmary and Kiedrowski: Selection versus Coexistence of Parabolic Replicators Spreading on Surfaces (2000)

12__21.1. Nonequilibrium strategies in molecular evolution (Braun)

Paper: (Braun)
Kuhn: Model Consideration for the Origin of Life (1976)
Kuhn: Diversified World: Drive to Life’s Origin?! (2003)
Braun: Convective PCR (2003)Braun: Hydrothermal Accumulation (2007)
Matsuno: Elongation by repetitive fast cooling (1999)

13__28.1. Towards exponential replicators (Braun)

* Paper: (Kalle Bamberg, Fritz)
Eigen: Spiegelman updated (1998)
Kiedrowsky: SPREAD (1993)
Ellington: Exponential growth by cross-catalytic cleavage of deoxyribozymogens (2003)

14__4.2. Strategies towards artificial cells (Simmel)

* Paper: (Angeliki Tsokou. Fritz)
Luisi: Approaches to semi-synthetic minimal cells: a review (2005)
Church: Towards synthesis of a minimal cell (2006)
Noireaux: A vesicle bioreactor as a step toward an artificial cell assembly (2004)

15__11.2. Open discussion: where to go with experiments? (Braun/Simmel)

Verantwortlich für den Inhalt: Dieter Braun