Humboldt-Universität zu Berlin - Department of Biology

Teaching

 

Winter Term 2014/15

Lab "Python for the Life Sciences"

Time: Tue, Feb 17th 2015 - Fri, Feb 27th 2015, 10.00 am
Place: Computer Pool Neubau Invalidenstraße 42
 

Lecture "Molecular Biophysics" (BioPhysics I)

Date Topic Slides
25./26.11.2014 Protein Folding Kinetics & Thermodynamics [PDF]
06./07.01.2015 Fluorescence [PDF]
13./14.01.2015 Hydrodynamic Methods [PDF]
20./21.01.2015 Of Heat, Atoms, Forces and Light [PDF]
 

Summer Term 2014

Lecture "Synthetic Biology" (BioPhysics XIV)

Monday 4 pm, Invalidenstraße 42, seminar room 312a
No. Date Topic Lecturer Slides
1 14.04.2014 Introduction, History & Ethics Möglich [PDF]
[DFG paper]
-- 21.04.2014 Easter Monday - no lecture -- --
2 28.04.2014 Biological Databases & Tools Möglich [PDF]
3 05.05.2014 Bioconjugate Chemistry & Total Protein Synthesis Möglich [PDF]
4 12.05.2014 DNA Manipulation and Libraries Möglich [PDF]
-- 19.05.2014 Conference travel - keine Vorlesung -- --
5 26.05.2014 Laboratory-directed Evolution Möglich [PDF]
6 02.06.2014 Incorporation of Non-canonical Amino Acids
Technische Universität Berlin, Building L, Room 009
Begin 4.15 pm
Budisa [PDF]

German: [PDF]

-- 09.06.2014 Pentecost - no lecture -- --
7 16.06.2014 Synthetic Signal Receptors & Optogenetics Möglich [PDF]
8 23.06.2014 De novo Proteins and Enzymes Möglich [PDF]
9 30.06.2014 DNA Computation & Origami Möglich [PDF]
10 07.07.2014 Transcriptional Control & Gene-regulatory Networks Möglich [PDF]
11 14.07.2014 Metabolic Engineering & Synthetic Life Möglich [PDF]
 

Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)

Time window A 14.04.-25.04.2014.
Start of course Monday, 14.04.2014
First meeting Monday, 14.04.2014, 9.30 am s. t. Room 304.
 

Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)

The seminar is one component of the module 'Synthetic Biology', and each participant should present one of the papers from the below list. Pending prior approval, the seminar can also be qualified for other biophysics modules. Please choose a topic and date you are interested in, and send me an email. First come, first serve; other papers are acceptable pending approval. The seminar starts on 25.04.2014.

Friday 8.15 am, Invalidenstraße 42, seminar room 312a
 
Date Paper Lecturer(s) Link Slides
25.04.2014 Annaluru, N. et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344(6179), 55-58. A.M. [Link] [PDF]
02.05.2014 Tag nach 1. Mai -- kein Seminar -- -- --
09.05.2014 Okamoto, R., Mandal, K., Sawaya, M.R., Kajihara, Y., Yeates, T.O., Kent, S.B. (2014) (Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis. Angew Chemie Int Ed in press

Deng, F.K., Zhang, L., Wang, Y.T., Schneewind, O., Kent, S.B. (2014) Total Chemical Synthesis of the Enzyme Sortase AΔN59 with Full Catalytic Activity. Angew Chemie Int Ed in press

Okamoto, R., Mandal, K., Ling, M., Luster, A.D., Kajihara, Y., Kent, S.B. (2014) Total Chemical Synthesis and Biological Activities of Glycosylated and Non-Glycosylated Forms of the Chemokines CCL1 and Ser-CCL1. Angew Chemie Int Ed in press

A.M. [Link]

[Link]

[Link]

[PDF]
16.05.2014 Geu-Flores, F., Nour-Eldin, H.H., Nielsen, M.T., Halkier, B.A. (2007) USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res 35(7), e55.

Villiers, B.R., Stein, V., Hollfelder, F. (2010) USER friendly DNA recombination (USERec): a simple and flexible near homology-independent method for gene library construction. Protein Eng Des Sel 23(1), 1-8.

Salomonsen, B., Mortensen, U.H., Halkier, B.A. (2014) USER-derived cloning methods and their primer design. Methods Mol Biol 852, 59-72.

Andrea Dotzler [Link]

[Link]

[Link]
(Printed version of bottom reference available from A.M.)

[PDF]
23.05.2014 kein Seminar -- -- --
30.05.2014 Ai, H.W., Baird, M.A., Shen, Y., Davidson, M.W., Campbell, R.E. (2014) Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications. Nat Protoc 9(4), 910-928.

Filonov, G.S., Piatkevich, K.D., Ting, L.M., Zhang, J., Kim, K., Verkhusha, V.V. (2011) Bright and stable near-infrared fluorescent protein for in vivo imaging. Nat Biotechnol 29(8), 757-761.

Shcherbakova, D.M., Verkhusha, V.V. (2013) Near-infrared fluorescent proteins for multicolor in vivo imaging. Nat Methods 10(8), 751-754.

Daniel Pawliczek [Link]

[Link]

[Link]

[PDF]
  Yi, L., Gebhard, M.C., Li, Q., Taft, J.M., Georgiou, G., Iverson, B.L. (2013) Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries. Proc Natl Acad Sci U S A 110(18), 7229-7234. N.N. [Link] [PDF]
06.06.2014 Isaacs, F.J., Carr, P.A., Wang, H.H., Lajoie, M.J., Sterling, B., Kraal, L., Tolonen, A.C., Gianoulis, T.A., Goodman, D.B., Reppas, N.B., Emig, C.J., Bang, D., Hwang, S.J., Jewett, M.C., Jacobson, J.M., Church, G.M. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333(6040), 348-353.

Lajoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., Mercer, J.A., Wang, H.H., Carr, P.A., Mosberg, J.A., Rohland, N., Schultz, P.G., Jacobson, J.M., Rinehart, J., Church, G.M., Isaacs, F.J. (2013) Genomically recoded organisms expand biological functions. Science 342(6156), 357-360.

Marlene Lindner [Link]

[Link]

[PDF]
13.06.2014 Pfingstwoche -- kein Seminar -- -- --
20.06.2014 Yang, X., Jost, A.P., Weiner, O.D., Tang, C. (2014) A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol Biol Cell 24(15), 2419-2430. Malte Hilsch [Link] [PDF]
  Motta-Mena, L.B., Reade, A., Mallory, M.J., Glantz, S., Weiner, O.D., Lynch, K.W., Gardner, K.H. (2014) An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat Chem Biol 10(3), 196-202. Isabel Kuhnert [Link]

[PDF]

[PDF]
27.06.2014 Tinberg, C.E., Khare, S.D., Dou, J., Doyle, L., Nelson, J.W., Schena, A., Jankowski, W., Kalodimos, C.G., Johnsson, K., Stoddard, B.L., Baker, D. (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501(7466), 212-216. Lars Zerbe [Link] [PDF]
  Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T.B., Montelione, G.T., Baker, D. (2012) Principles for designing ideal protein structures. Nature 491(7423), 222-227. Robert-William Welke [Link] [PDF]
04.07.2014 Iinuma, R., Ke, Y., Jungmann, R., Schlichthaerle, T., Woehrstein, J.B., Yin, P. (2014) Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344(6179), 65-69. Ferdinand Krupp [Link] [PDF]
  Chen, H., Weng, T.W., Riccitelli, M., Cui, Y., Irudayaraj, J., Choi, J.H. (2014) Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of their Folding and Unfolding Reconfiguration. J Am Chem Soc in press Wiebke Schmidt [Link] [PDF]
11.07.2014 Wang, B.L., Ghaderi, A., Zhou, H., Agresti, J., Weitz, D.A., Fink, G.R., Stephanopoulos, G. (2014) Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol in press Anke Vollertsen [Link] [PDF]
  Ling, H., Teo, W., Chen, B., Leong, S.S., Chang, M.W. (2014) Microbial tolerance engineering toward biochemical production: from lignocellulose to products. Curr Opin Biotechnol 29C, 99-106.

Wang, X., Yomano, L.P., Lee, J.Y., York, S.W., Zheng, H., Mullinnix, M.T., Shanmugam, K.T., Ingram, L.O. (2013) Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci U S A 110(10), 4021-4026.

Tina Jaenicke [Link]

[Link]

[PDF]
18.07.2014 Malyshev, D.A., Dhami, K., Lavergne, T., Chen, T., Dai, N., Foster, J.M., Corrêa Jr, I.R., Romesberg, F.E. (2014) A semi-synthetic organism with an expanded genetic alphabet. Nature in press Deborah Stier [Link] [PDF]
  Xiao, H., Chatterjee, A., Choi, S.H., Bajjuri, K.M., Sinha, S.C., Schultz, P.G. (2014) Genetic incorporation of multiple unnatural amino acids into proteins in mammalian cells. Angew Chem Int Ed Engl 52(52), 14080-14083.

Xiao, H., Peters, F.B., Yang, P.Y., Reed, S., Chittuluru, J.R., Schultz, P.G. (2014) Genetic Incorporation of Histidine Derivatives Using an Engineered Pyrrolysyl-tRNA Synthetase. ACS Chem Biol in press

Maximiliano Ancina Möller [Link]

[Link]

[PDF]
 

Lab "Biophysics" (B.Sc. class 3110022)

Spektroskopische Charakterisierung von Blaulichtrezeptorproteinen [PDF]
Analyse von Proteinstrukturen mit PyMOL [PDF]
 

Winter Term 2013/14

Lab "Python for the Life Sciences"

Time: Tue, Feb 4th 2014 - Fri, Feb 14th 2014
Place: Computer Pool Neubau Invalidenstraße 42
More info will be available here.
 

Lecture "Molecular Biophysics" (BioPhysics I)

Date Topic Slides
26./27.11.2013 Protein Folding Kinetics & Thermodynamics [PDF]
07./08.01.2014 Fluorescence [PDF]
14./15.01.2014 Hydrodynamic Methods [PDF]
21./22.01.2014 Of Heat, Atoms, Forces and Light [PDF]
 

Summer Term 2013

Lecture "Synthetic Biology" (BioPhysics XIV)

Monday 4 pm, Invalidenstraße 42, seminar room 312a
 
No. Date Topic Lecturer Slides
1 08.04.2013 Introduction, History & Ethics Möglich [PDF]
2 15.04.2013 Biological Databases & Tools Möglich [PDF]
3 22.04.2013 Incorporation of Non-canonical Amino Acids
Technical University Berlin, Building L, Room 009
Budisa [PDF]
4 29.04.2013 Bioconjugate Chemistry & Total Protein Synthesis Möglich [PDF]
5 06.05.2013 DNA Manipulation and Libraries Möglich [PDF]
6 13.05.2013 Laboratory-directed Evolution Möglich [PDF]
-- 20.05.2013 Pentecost - no lecture -- --
7 27.05.2013 Synthetic Signal Receptors & Optogenetics Möglich [PDF]
8 03.06.2013 De novo Proteins and Enzymes Möglich [PDF]
9 10.06.2013 DNA Computation & Origami Möglich [PDF]
10 17.06.2013 Transcriptional Control & Gene-regulatory Networks Möglich [PDF]
11 24.06.2013 Metabolic Engineering & Synthetic Life Möglich [PDF]

Students who are enrolled in the module "Synthetic Biology" have to submit a research proposal. Details will be discussed, and instructions are available.
 

Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)

Time frame A, 09.04.-20.04.2013. First meeting Tue, 02.04.2013 10.00 s. t. room 304.
 

Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)

The seminar is one component of the module 'Synthetic Biology', and each participant should present one of the papers from the below list. Pending prior approval, the seminar can also be qualified for other biophysics modules. Please choose a topic and date you are interested in, and send me an email. First come, first serve; other papers are acceptable pending approval. The seminar starts on 26.04.2013.

Friday 8.15 am, Invalidenstraße 42, seminar room 312a
 
Date Topic Lecturer(s) Link Slides
26.04.2013 Chatterjee, A., Xiao, H., Schultz, P.G. (2012) Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 109(37), 14841-14846.
Grunbeck, A., Huber, T., Sakmar, T.P. (2012) Mapping a ligand binding site using genetically encoded photoactivatable crosslinkers. Methods Enzymol 520, 307-322.
A.M. [Link]
[PDF]
[PDF]
03.05.2013 Yeates, T.O., Kent, S.B. (2012) Racemic Protein Crystallography. Annu Rev Biophys 41, 21-41
Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angewandte Chemie 51(6), 1481-6
N.N.
Jakob Kottmann
[Link]
[Link]
[PDF]
10.05.2013 Gibson, D.G., Young, L., Chuang, R.Y., Venter, J.C., Hutchison, C.A. 3rd, Smith, H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6(5), 343-345.
Gibson, D.G. (2011) Enzymatic assembly of overlapping DNA fragments. Methods Enzymol 498, 349-361.

Cancelled!
N.N. [Link]
[PDF]
[PDF]
17.05.2013 Davids, T., Schmidt, M., Böttcher, D., Bornscheuer, U.T. (2013) Strategies for the discovery and engineering of enzymes for biocatalysis. Curr Opin Chem Biol in press
Larman, H.B., Xu, G.J., Pavlova, N.N., Elledge, S.J. (2012) Construction of a rationally designed antibody platform for sequencing-assisted selection. Proc Natl Acad Sci U S A 109(45), 18523-18528.
Jürgen Arndt
Manuela Denz
[PDF]
[Link]
[PDF]
24.05.2013 Extra day after Pentecost -- -- --
31.05.2013 Müller, K., Engesser, R., Metzger, S., Schulz, S., Kämpf, M.M., Busacker, M., Steinberg, T., Tomakidi, P., Ehrbar, M., Nagy, F., Timmer, J., Zubriggen, M.D., Weber W. (2013) A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells. Nucleic Acids Res in press Roman Scholz [Link] [PDF]
07.06.2013 Kiss, G., Celebi-Ölçüm, N., Moretti, R., Baker, D., Houk, K.N. Computational Enzyme Design. Angew Chem Int Ed Engl in press Rahel Frick [Link] [PDF]
14.06.2013 Rajendran, A., Endo, M., Hidaka, K., Sugiyama, H. (2013) Direct and real-time observation of rotary movement of a DNA nanomechanical device. J Am Chem Soc 135(3), 1117-1123.
Langecker, M., Arnaut, V., Martin, T.G., List, J., Renner, S., Mayer, M., Dietz, H., Simmel, F.C. (2012) Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338(6109), 932-936.
Laura Zeugner
Hu Jingjun
[Link]
[Link]
[PDF]
21.06.2013 Bugaj, L.J., Choksi, A.T., Mesuda, C.K., Kane, R.S., Schaffer, D.V. (2013) Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods 10(3), 249-252.
Lee, J.W., Na, D., Park, J.M., Lee, J., Choi, S., Lee, S.Y. (2012) Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 8(6), 536-546.
Jardine, J., Julien, J.P., Menis, S., Ota, T., Kalyuzhniy, O., McGuire, A., Sok, D., Huang, P.S., Macpherson, S., Jones, M., Nieusma, T., Mathison, J., Baker, D., Ward, A.B., Burton, D.R., Stamatatos, L., Nemazee, D., Wilson, I.A., Schief, W.R. (2013) Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors. Science in press
Julia Katharina Schlichting
Tobias Wörner
Ali Saitov
[Link]
[PDF]
[Link]
[PDF]
28.06.2013 Ke, Y., Ong, L.L., Shih, W.M., Yin, P. (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338(6111), 1177-1183.
Kimoto, M., Yamashige, R., Matsunaga, K., Yokoyama, S., Hirao, I. (2013) Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat Biotechnol 31(5), 453-457.
Siuti, P., Yazbek, J., Lu, T.K. (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5), 448-452.
Benedikt Dänekamp
Jelena Pajovic
Christian Wienberg
[Link]
[Link]
[Link]
[PDF]
 

Lab "Biophysics" (B.Sc. course 3110022)

Spectroscopic Characterization of Blue-Light Photoreceptor Proteins [PDF]
Analysis of Protein Structures with PyMOL [PDF]
 

Winter Term 2012/13

Lab "Python for the Life Sciences"

Time: Feb 12th-22nd 2013
Place: Computer Pool Neubau Invalidenstraße 42
 

Lecture "Molecular Biophysics" (BioPhysics I)

Date Topic Slides
27./28.11.2012 Protein Folding Kinetics & Thermodynamics [PDF]
08./09.01.2013 Fluorescence [PDF]
15./16.01.2012 Hydrodynamic Methods & CD Spectroscopy [PDF]
05./06.02.2013 Of Heat, Atoms, Forces and Light [PDF]
 

Summer Term 2012

Lecture "Synthetic Biology" (BioPhysics XIV)

Nr. Date Topic Lecturer Slides
1 16.04.2012 Introduction, History & Ethics Möglich [PDF]
2 23.04.2012 Biological Databases & Tools Möglich [PDF]
3 30.04.2012 Incorporation of Non-canonical Amino Acids Budisa [PDF]
4 07.05.2012 Bioconjugate Chemistry & Total Protein Synthesis Möglich [PDF]
5 14.05.2012 DNA Manipulation and Libraries Möglich [PDF]
6 21.05.2012 Laboratory-directed Evolution Möglich [PDF]
-- 28.05.2012 Pfingsten - no lecture -- --
7 04.06.2012 Synthetic Signal Receptors & Optogenetics Möglich [PDF]
8 11.06.2012 De novo Proteins and Enzymes Möglich [PDF]
-- 18.06.2012 Business trip - no lecture -- --
9 25.06.2012 DNA Computation & Origami Möglich [PDF]
10 02.07.2012 Transcriptional Control & Gene-regulatory Networks Möglich [PDF]
11 09.07.2012 Metabolic Engineering & Synthetic Life Möglich [PDF]
 

Lab "Design and Characterization of Synthetic Photoreceptors" (BioPhysics XIV)

First meeting Mo, 14.05.2012 14.00 s. t. seminar room 312.

 

Seminar "Current Topics in Photobiology and Protein Design" (BioPhysics XIV)

Date Paper Presenter Link Slides
27.04.2012 More Databases & Tools for Structure Analysis Möglich n/a [PDF]
04.05.2012 Liu, C.C., Schultz, P.G. (2010) Adding new chemistries to the genetic code. Annu Rev Biochem 79:413-44
Ai, H.W. , Shen, W., Sagi, A., Chen, P.R., Schultz, P.G. (2011) Probing protein-protein interactions with a genetically encoded photo-crosslinking amino acid. ChemBioChem 12(12):1854-7
Möglich [Link]
[Link]
[PDF]
11.05.2012 Yeates, T.O., Kent, S.B. (2012) Racemic Protein Crystallography. Annu Rev Biophys 41:21-41
Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angewandte Chemie 51(6):1481-6

Cancelled
[Link]
[Link]
[PDF]
18.05.2012 Pinheiro, V.B., Taylor, A.I., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J.C., Wengel, J., Peak-Chew, S.Y., McLaughlin, S.H., Herdewijn, P., Holliger, P. (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336(6079):341-4
Joyce, G.F. (2012) Evolution. Toward an alternative biology. Science 336(6079):307-8
Jens Hahn [Link]
[Link]
[PDF]
25.05.2012 Luo, Y., Xia, Y. (2012) Selection of single-chain variable fragment antibodies against fenitrothion by ribosome display. Anal Biochem 421(1):130-7
Bornscheuer, U., Kazlauskas, R.J. (2011) Survey of protein engineering strategies. Curr Protoc Protein Sci Unit26.7
Sonja Minniberger [Link]
[Link]
[PDF]
01.06.2012 Extra Tag -- -- --
08.06.2012 Wang, X., Chen, X., Yang, Y. (2012) Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods 9(3):266-9
Lungu, O.I., Hallett, R.A., Choi, E.J., Aiken, M.J., Hahn, K.M., Kuhlman, B. (2012) Designing Photoswitchable Peptides Using the AsLOV2 Domain. Chem Biol 19(4):507-17
Robert Streeck
Philip Luxen
[Link]
[Link]
[PDF]
[PDF]
15.06.2012 Siegel, J.B., Zanghellini, A., Lovick, H.M., Kiss, G., Lambert, A.R., St Clair, J.L., Gallaher, J.L., Hilvert, D., Gelb, M.H., Stoddard, B.L., Houk, K.N., Michael, F.E., Baker, D. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329(5989):309-13
Khare, S.D., Kipnis, Y., Greisen, P. Jr, Takeuchi, R., Ashani, Y., Goldsmith, M., Song, Y., Gallaher, J.L., Silman, I., Leader, H., Sussman, J.L., Stoddard, B.L., Tawfik, D.S., Baker, D. (2012) Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat Chem Biol 8(3):294-300
Martha Braun
Frauke Dreyer
[Link]
[Link]
[PDF]
[PDF]
22.06.2012 Extra Tag -- -- --
29.06.2012 Kuzyk, A., Schreiber, R., Fan, Z., Pardatscher, G., Roller, E.M., Högele, A., Simmel, F.C., Govorov, A.O., Liedl, T. (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311-4
Douglas, S.M., Bachelet, I., Church, G.M. (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831-4
Christiane Grimm
Kristin Schmidt
[Link]
[Link]
[PDF]
[PDF]
06.07.2012 Dellomonaco, C., Clomburg, J.M., Miller, E.N., Gonzalez, R. (2011) Engineered reversal of the ß-oxidation cycle for the synthesis of fuels and chemicals. Nature 476(7360):355-9
Prindle, A., Samayoa, P., Razinkov, I., Danino, T., Tsimring, L.S., Hasty, J. (2011) A sensing array of radically coupled genetic 'biopixels'. Nature 481(7379):39-44
Julian Appelfeller
Tobias Kaufholz
[Link]
[Link]
[PDF]
[PDF]
13.07.2012 Wargacki, A.J., Leonard, E., Win, M.N., Regitsky, D.D., Santos, C.N., Kim, P.B., Cooper, S.R., Raisner, R.M., Herman, A., Sivitz, A.B., Lakshmanaswamy, A., Kashiyama, Y., Baker, D., Yoshikuni, Y. (2012) An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335(6066):308-13 Tom Lindtner [Link] [PDF]
 

Winter Term 2011/12

Lab "Python for the Life Sciences"

 

Lecture "Molecular Biophysics" (BioPhysics I)

Date Topic Slides
10./11.01.2012 Protein Folding Kinetics & Thermodynamics [PDF]
17./18.01.2012 Fluorescence [PDF]
07./08.02.2012 Hydrodynamic Methods & CD Spectroscopy [PDF]
 

Summer Term 2011

Lecture "Synthetic Biology" (BioPhysics IV or VII)

Nr. Date Topic Lecturer Slides
1 11.04.2011 Introduction, History & Ethics Möglich [PDF]
2 18.04.2011 Biological Databases & Tools Möglich [PDF]
3 02.05.2011 Incorporation of Non-canonical Amino Acids Budisa [PDF]
4 09.05.2011 Bioconjugate Chemistry & Total Protein Synthesis Möglich [PDF]
5 16.05.2011 DNA Manipulation and Libraries Möglich [PDF]
6 23.05.2011 Laboratory-directed Evolution Möglich [PDF]
7 30.05.2011 Synthetic Signal Receptors & Optogenetics Möglich [PDF]
8 06.06.2011 De novo Proteins and Enzymes Möglich [PDF]
-- 13.06.2011 Pfingsten - no lecture -- --
9 20.06.2011 Transcriptional Control & Gene-regulatory Networks Möglich [PDF]
10 27.06.2011 Metabolic Engineering & Synthetic Life Möglich [PDF]
11 04.07.2011 Student Presentations -- --
12 11.07.2011 Student Presentations -- --


Important Note
To get credit for this lecture, you have to give a seminar presentation in the last two weeks of this course. You can team up as groups of 2-3 people and choose any paper that is relevant to any unit of this lecture series. Please prepare a 10-15 minutes presentation. If you have questions or need a suggestion for a suitable paper, please contact me by email.

In the below table please find the scheduled seminar presentations:
Date Students Paper Slides
04.07.2011 Chang Yan
Claudia Beck
Fleishman et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332:816-821 [Link] --
04.07.2011 Stefan Greulich
Peer Schrapers
Mascarello et al. (2010) Inhibition of Mycobacterium tuberculosis tyrosine phosphatase PtpA by synthetic chalcones: kinetics, molecular modeling, toxicity and effect on growth. Bioorg Med Chem 18:3783-3789 [Link] [PDF]
04.07.2011 Damian Pawolski
Friederike Knipping
Blankenship et al. (2011) Comparing photosynthetic and photovoltaic efficiencies and recognizing the potential for improvement. Science 332:805-809 [Link] --
04.07.2011 Annabell Hillenbrand
Ferdinand Greiss
E. glowli - iGEM project Team Cambridge 2010 [Link] --
11.07.2011 Roman Fudim
Jonas Wietek
Helena Steinocher
Sievers et al. (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature doi:10.1038/nature10154 [Link] --
11.07.2011 Hikan Kobayashi Basu et al. (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130-1134 [Link] --
11.07.2011 Martin Weiland
Anne Pelikan
Jedrzej Blaskievicz
Anderson et al. (2006) Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 355:619-627 [Link] --
11.07.2011 Anna Erzberger
Christopher Wolff
Ro et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940-943 [Link] --
 

Lab "Design and Characterization of Synthetic Photoreceptors" (BPC1)

First meeting Mo, 27.06.2011 10.00 s. t. seminar room 312.
 

Winter Term 2010/11

Lab "Python for the Life Sciences"